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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.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O"}],"title":"Local adaptation, genetic load and extinction in metapopulations","citation":{"chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380"}],"page":"183","date_created":"2023-12-26T22:49:53Z","date_published":"2024-01-19T00:00:00Z","doi":"10.15479/at:ista:14711","year":"2024","has_accepted_license":"1","day":"19","oa":1,"publisher":"Institute of Science and Technology Austria"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","mla":"Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821","apa":"Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024."},"title":"Adaptive hierarchical representations in the hippocampus","article_processing_charge":"No","author":[{"last_name":"Chiossi","full_name":"Chiossi, Heloisa","first_name":"Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"day":"19","year":"2024","has_accepted_license":"1","date_created":"2024-01-16T14:25:21Z","doi":"10.15479/at:ista:14821","date_published":"2024-01-19T00:00:00Z","page":"89","publisher":"Institute of Science and Technology Austria","ddc":["570"],"date_updated":"2024-02-01T09:50:29Z","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"file_date_updated":"2024-01-19T11:04:05Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"_id":"14821","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_id":"14838","checksum":"d3fa3de1abd5af5204c13e9d55375615","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2024-01-19T11:04:05Z","file_name":"PhD_Thesis_190124.docx","date_updated":"2024-01-19T11:04:05Z","file_size":8656268,"creator":"hchiossi"},{"file_name":"PhD_Thesis_190124.pdf","date_created":"2024-01-19T11:03:59Z","creator":"hchiossi","file_size":6567275,"date_updated":"2024-01-19T11:03:59Z","embargo":"2025-01-19","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","file_id":"14839","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"oa_version":"Published Version","month":"01","alternative_title":["ISTA Thesis"]},{"keyword":["Theoretical biology","Optimality","Evolution","Information"],"status":"public","type":"dissertation","_id":"15020","file_date_updated":"2024-02-23T14:20:16Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"ddc":["576","519"],"date_updated":"2024-03-06T14:22:52Z","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7553"},{"status":"public","id":"12081","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7606"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","file_size":7102089,"date_updated":"2024-02-23T13:50:53Z","creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","date_created":"2024-02-23T13:50:53Z"},{"file_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","creator":"mhledik","file_size":14014790,"date_updated":"2024-02-23T14:20:16Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_id":"15022","relation":"source_file","access_level":"closed","content_type":"application/zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"title":"Genetic information and biological optimization","article_processing_charge":"No","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2024-02-23T14:02:04Z","doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","page":"158","day":"23","year":"2024","has_accepted_license":"1"},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"jchen","file_size":11271363,"date_updated":"2024-03-12T07:12:17Z","file_name":"Thesis_Jingjing CHEN.docx","date_created":"2024-03-11T14:10:58Z","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"db4947474ffa271e66c254b6fe876a55","file_id":"15104"},{"checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_id":"15105","embargo":"2024-04-01","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file","date_created":"2024-03-11T14:11:06Z","file_name":"Thesis_Jingjing CHEN_merged.pdf","date_updated":"2024-03-11T14:11:06Z","file_size":16627311,"creator":"jchen"}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"14843","status":"public"}]},"_id":"15101","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)"},"type":"dissertation","status":"public","date_updated":"2024-03-14T13:14:19Z","supervisor":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T07:12:17Z","publisher":"Institute of Science and Technology Austria","year":"2024","has_accepted_license":"1","day":"11","page":"84","date_created":"2024-03-11T10:09:54Z","date_published":"2024-03-11T00:00:00Z","doi":"10.15479/at:ista:15101","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"last_name":"Chen","full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse"},{"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_id":"15112","creator":"scultrer","file_size":4106872,"date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","date_created":"2024-03-14T08:55:07Z"},{"file_id":"15113","checksum":"bcbd213490f5a7e68855a092bbce93f1","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2024-03-14T08:56:24Z","file_name":"Thesis (1).zip","date_updated":"2024-03-14T14:14:35Z","file_size":4746234,"creator":"scultrer"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11660"},{"relation":"part_of_dissertation","id":"11658","status":"public"},{"status":"public","id":"13182","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"15090"},{"status":"public","id":"15091","relation":"part_of_dissertation"},{"id":"15093","status":"public","relation":"part_of_dissertation"}]},"_id":"15094","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","date_updated":"2024-03-20T09:36:57Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"ddc":["514","500","516"],"file_date_updated":"2024-03-14T14:14:35Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"oa":1,"publisher":"Institute of Science and Technology Austria","year":"2024","has_accepted_license":"1","day":"08","page":"108","date_created":"2024-03-08T15:28:10Z","date_published":"2024-03-08T00:00:00Z","doi":"10.15479/at:ista:15094","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Discretization in Geometry and Dynamics"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano"}],"title":"Persistence and Morse theory for discrete geometric structures"},{"file":[{"file_name":"Burnett_Thesis_2023.docx","date_created":"2023-03-08T15:08:46Z","creator":"lburnett","file_size":23029260,"date_updated":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_id":"12717","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z","file_size":11959869,"date_updated":"2023-03-08T15:08:46Z","creator":"lburnett"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","ec_funded":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"month":"03","alternative_title":["ISTA Thesis"],"ddc":["599","573"],"supervisor":[{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"date_updated":"2023-04-05T10:59:04Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file_date_updated":"2023-03-08T15:08:46Z","_id":"12716","status":"public","type":"dissertation","day":"10","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:12716","date_published":"2023-03-10T00:00:00Z","date_created":"2023-03-08T15:19:45Z","page":"178","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716."},"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","author":[{"first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura"}],"article_processing_charge":"No","project":[{"name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"page":"115","date_published":"2023-04-06T00:00:00Z","doi":"10.15479/at:ista:12809","date_created":"2023-04-06T07:54:09Z","has_accepted_license":"1","year":"2023","day":"06","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Alcarva, Catarina","last_name":"Alcarva","first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","citation":{"ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-04-07","checksum":"35b5997d2b0acb461f9d33d073da0df5","file_id":"12814","file_size":9881969,"date_updated":"2023-04-07T06:16:06Z","creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_created":"2023-04-07T06:16:06Z"},{"date_updated":"2023-04-07T06:17:11Z","file_size":44201583,"creator":"cchlebak","date_created":"2023-04-07T06:17:11Z","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","content_type":"application/pdf","access_level":"closed","relation":"source_file","file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc"},{"file_name":"Thesis_CatarinaAlcarva_final.docx","date_created":"2023-04-07T06:18:05Z","file_size":84731244,"date_updated":"2023-04-07T06:18:05Z","creator":"cchlebak","file_id":"12816","checksum":"0317bf7f457bb585f99d453ffa69eb53","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"04","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"oa_version":"Published Version","file_date_updated":"2023-04-07T06:18:05Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"supervisor":[{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-04-26T12:16:56Z","ddc":["570"],"type":"dissertation","status":"public","_id":"12809"},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","article_processing_charge":"No","author":[{"orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023."},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-04-14T14:56:04Z","doi":"10.15479/at:ista:12826","date_published":"2023-04-18T00:00:00Z","page":"106","day":"18","year":"2023","has_accepted_license":"1","status":"public","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)"},"type":"dissertation","_id":"12826","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"file_date_updated":"2023-04-20T09:26:51Z","ddc":["570","571"],"date_updated":"2023-06-23T09:47:36Z","supervisor":[{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"ec_funded":1,"language":[{"iso":"eng"}],"file":[{"checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","date_created":"2023-04-20T09:14:38Z","file_size":14507243,"date_updated":"2023-04-20T09:26:51Z","creator":"vpokusae"},{"success":1,"file_id":"12858","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","date_created":"2023-04-20T09:14:44Z","file_size":10090711,"date_updated":"2023-04-20T09:14:44Z","creator":"vpokusae"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]}},{"oa_version":"Published Version","abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"03","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","creator":"vkravchu","date_updated":"2023-04-19T14:33:41Z","file_size":6071553,"file_id":"12852","checksum":"5ebb6345cb4119f93460c81310265a6d","embargo":"2024-04-20","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"local"},{"embargo":"2024-04-20","file_id":"12853","checksum":"c12055c48411d030d2afa51de2166221","embargo_to":"local","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","date_created":"2023-04-19T14:33:52Z","file_size":19468766,"date_updated":"2023-04-20T07:02:59Z","creator":"vkravchu"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"12138","status":"public"}]},"_id":"12781","status":"public","type":"dissertation","ddc":["570","572"],"date_updated":"2023-08-04T08:54:51Z","supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"file_date_updated":"2023-04-20T07:02:59Z","publisher":"Institute of Science and Technology Austria","day":"23","year":"2023","has_accepted_license":"1","date_created":"2023-03-31T12:24:42Z","doi":"10.15479/at:ista:12781","date_published":"2023-03-23T00:00:00Z","page":"127","project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria."},"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","article_processing_charge":"No","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav"}]},{"alternative_title":["ISTA Thesis"],"month":"05","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"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11458"},{"relation":"part_of_dissertation","status":"public","id":"13053"},{"id":"12299","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_size":2152072,"date_updated":"2023-05-24T16:11:16Z","creator":"epeste","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","date_created":"2023-05-24T16:11:16Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"6b3354968403cb9d48cc5a83611fb571","file_id":"13087"},{"file_size":1658293,"date_updated":"2023-05-24T16:12:59Z","creator":"epeste","file_name":"PhD_Thesis_APeste.zip","date_created":"2023-05-24T16:12:59Z","content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"13088","checksum":"8d0df94bbcf4db72c991f22503b3fd60"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","_id":"13074","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"file_date_updated":"2023-05-24T16:12:59Z","supervisor":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-04T10:33:27Z","ddc":["000"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"147","date_published":"2023-05-23T00:00:00Z","doi":"10.15479/at:ista:13074","date_created":"2023-05-23T17:07:53Z","has_accepted_license":"1","year":"2023","day":"23","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"}],"article_processing_charge":"No","title":"Efficiency and generalization of sparse neural networks","citation":{"ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"}]