[{"publication_status":"published","author":[{"full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Sricharan, A. R.","last_name":"Sricharan","first_name":"A. R."},{"full_name":"Steiner, Teresa Anna","last_name":"Steiner","first_name":"Teresa Anna"}],"department":[{"_id":"MoHe"}],"external_id":{"arxiv":["2408.11637"],"isi":["001545634500040"]},"date_created":"2024-09-29T22:01:38Z","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"alternative_title":["LIPIcs"],"type":"conference","month":"09","file":[{"creator":"dernst","checksum":"c08b41c896e4d8c69570044808b40e0b","success":1,"file_id":"18166","file_size":973917,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2024_LIPICs_HenzingerM.pdf","date_updated":"2024-10-01T10:07:14Z","date_created":"2024-10-01T10:07:14Z"}],"arxiv":1,"corr_author":"1","isi":1,"title":"Private counting of distinct elements in the turnstile model and extensions","project":[{"grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Efficient algorithms"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"oa":1,"citation":{"mla":"Henzinger, Monika, et al. “Private Counting of Distinct Elements in the Turnstile Model and Extensions.” <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, vol. 317, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>.","ieee":"M. Henzinger, A. R. Sricharan, and T. A. Steiner, “Private counting of distinct elements in the turnstile model and extensions,” in <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, London, United Kingdom, 2024, vol. 317.","short":"M. Henzinger, A.R. Sricharan, T.A. Steiner, in:, International Conference on Approximation Algorithms for Combinatorial Optimization Problems , Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ista":"Henzinger M, Sricharan AR, Steiner TA. 2024. Private counting of distinct elements in the turnstile model and extensions. International Conference on Approximation Algorithms for Combinatorial Optimization Problems . APPROX: Conference on Approximation Algorithms for Combinatorial Optimization Problems, LIPIcs, vol. 317, 40.","ama":"Henzinger M, Sricharan AR, Steiner TA. Private counting of distinct elements in the turnstile model and extensions. In: <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>. Vol 317. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>","chicago":"Henzinger, Monika, A. R. Sricharan, and Teresa Anna Steiner. “Private Counting of Distinct Elements in the Turnstile Model and Extensions.” In <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, Vol. 317. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>.","apa":"Henzinger, M., Sricharan, A. R., &#38; Steiner, T. A. (2024). Private counting of distinct elements in the turnstile model and extensions. In <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i> (Vol. 317). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>"},"date_updated":"2025-12-02T13:47:16Z","file_date_updated":"2024-10-01T10:07:14Z","scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","_id":"18156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"40","day":"16","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct,No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nTeresa Anna Steiner: Supported by a research grant (VIL51463) from VILLUM FONDEN.","oa_version":"Published Version","ddc":["000"],"year":"2024","doi":"10.4230/LIPIcs.APPROX/RANDOM.2024.40","conference":{"end_date":"2024-08-30","location":"London, United Kingdom","start_date":"2024-08-27","name":"APPROX: Conference on Approximation Algorithms for Combinatorial Optimization Problems"},"quality_controlled":"1","has_accepted_license":"1","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773485"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Privately counting distinct elements in a stream is a fundamental data analysis problem with many applications in machine learning. In the turnstile model, Jain et al. [NeurIPS2023] initiated the study of this problem parameterized by the maximum flippancy of any element, i.e., the number of times that the count of an element changes from 0 to above 0 or vice versa. They give an item-level (ε,δ)-differentially private algorithm whose additive error is tight with respect to that parameterization. In this work, we show that a very simple algorithm based on the sparse vector technique achieves a tight additive error for item-level (ε,δ)-differential privacy and item-level ε-differential privacy with regards to a different parameterization, namely the sum of all flippancies. Our second result is a bound which shows that for a large class of algorithms, including all existing differentially private algorithms for this problem, the lower bound from item-level differential privacy extends to event-level differential privacy. This partially answers an open question by Jain et al. [NeurIPS2023]."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"volume":317,"date_published":"2024-09-16T00:00:00Z","publication":"International Conference on Approximation Algorithms for Combinatorial Optimization Problems ","intvolume":"       317"},{"has_accepted_license":"1","quality_controlled":"1","doi":"10.5802/jep.270","publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"article_type":"original","ddc":["510"],"oa_version":"Published Version","year":"2024","intvolume":"        11","date_published":"2024-01-01T00:00:00Z","publication":"Journal de l'Ecole Polytechnique - Mathematiques","volume":11,"language":[{"iso":"eng"}],"article_processing_charge":"Yes","publisher":"Ecole Polytechnique","abstract":[{"text":"We study the geometry of Poisson point processes from the point of view of optimal transport and Ricci lower bounds. We construct a Riemannian structure on the space of point processes and the associated distance W that corresponds to the Benamou–Brenier variational formula. Our main tool is a non-local continuity equation formulated with the difference operator. The closure of the domain of the relative entropy is a complete geodesic space, when endowed with \r\nW. The geometry of this non-local infinite-dimensional space is analogous to that of spaces with positive Ricci curvature. Among others: (a) the Ornstein–Uhlenbeck semi-group is the gradient flow of the relative entropy; (b) the Poisson space has an entropic Ricci curvature bounded from below by 1; (c) W satisfies an HWI inequality.","lang":"eng"},{"text":"Nous étudions la géométrie des processus ponctuels de Poisson à travers le prisme du transport optimal et de la minoration de la courbure de Ricci. Nous construisons une structure\r\nriemannienne sur l’espace des processus ponctuels et la distance associée W qui concorde avec la formulation variationnelle de Benamou–Brenier. Notre analyse repose sur une équation de continuité non locale définie à l’aide de l’opérateur de différence. La fermeture du domaine de l’entropie relative, équipé de W, est un espace géodésique complet. La géométrie de cet espace non local et de dimension infinie est analogue à celle des espaces à courbure de Ricci strictement positive. Entre autres : (a) le semi-groupe d’Ornstein–Uhlenbeck est le flot du gradient de l’entropie relative ; (b) l’espace de Poisson a une courbure de Ricci entropique minorée par 1 ; (c) W satisfait une inégalité HWI.","lang":"fre"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","file_size":1250553,"checksum":"5a51da5fb5f7fcaada378d43444cced8","success":1,"file_id":"18164","creator":"dernst","date_updated":"2024-10-01T07:31:56Z","date_created":"2024-10-01T07:31:56Z","file_name":"2024_JourEcolePolytechniqueMath_DelloSchiavo.pdf","relation":"main_file","access_level":"open_access"}],"page":"957-1010","type":"journal_article","month":"01","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Herry, Ronan","last_name":"Herry","first_name":"Ronan"},{"last_name":"Suzuki","first_name":"Kohei","full_name":"Suzuki, Kohei"}],"publication_status":"published","external_id":{"isi":["001367254000003"],"arxiv":["2303.00398"]},"date_created":"2024-09-29T22:01:38Z","department":[{"_id":"JaMa"}],"_id":"18158","file_date_updated":"2024-10-01T07:31:56Z","scopus_import":"1","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Wasserstein geometry and Ricci curvature bounds for Poisson spaces","corr_author":"1","isi":1,"arxiv":1,"date_updated":"2025-09-08T09:50:50Z","oa":1,"citation":{"ieee":"L. Dello Schiavo, R. Herry, and K. Suzuki, “Wasserstein geometry and Ricci curvature bounds for Poisson spaces,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 11. Ecole Polytechnique, pp. 957–1010, 2024.","mla":"Dello Schiavo, Lorenzo, et al. “Wasserstein Geometry and Ricci Curvature Bounds for Poisson Spaces.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 11, Ecole Polytechnique, 2024, pp. 957–1010, doi:<a href=\"https://doi.org/10.5802/jep.270\">10.5802/jep.270</a>.","ista":"Dello Schiavo L, Herry R, Suzuki K. 2024. Wasserstein geometry and Ricci curvature bounds for Poisson spaces. Journal de l’Ecole Polytechnique - Mathematiques. 11, 957–1010.","short":"L. Dello Schiavo, R. Herry, K. Suzuki, Journal de l’Ecole Polytechnique - Mathematiques 11 (2024) 957–1010.","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, and Kohei Suzuki. “Wasserstein Geometry and Ricci Curvature Bounds for Poisson Spaces.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2024. <a href=\"https://doi.org/10.5802/jep.270\">https://doi.org/10.5802/jep.270</a>.","ama":"Dello Schiavo L, Herry R, Suzuki K. Wasserstein geometry and Ricci curvature bounds for Poisson spaces. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2024;11:957-1010. doi:<a href=\"https://doi.org/10.5802/jep.270\">10.5802/jep.270</a>","apa":"Dello Schiavo, L., Herry, R., &#38; Suzuki, K. (2024). Wasserstein geometry and Ricci curvature bounds for Poisson spaces. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.270\">https://doi.org/10.5802/jep.270</a>"}},{"acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt), the Singapore Ministry of Education (MOE) Academic Research Fund (AcRF) Tier 1 grant, Google Research Award 2023 and the SBI Foundation Hub for Data and Analytics.","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18159","scopus_import":"1","date_updated":"2025-04-14T07:52:46Z","oa":1,"citation":{"ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties,” in <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, Jeju, Korea, 2024, pp. 3–12.","mla":"Akshay, S., et al. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2024. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 3–12.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12.","chicago":"Akshay, S, Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, 3–12. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In: <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:3-12. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2024). Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i> (pp. 3–12). Jeju, Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>"},"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"title":"Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties","corr_author":"1","arxiv":1,"page":"3-12","month":"09","type":"conference","status":"public","external_id":{"arxiv":["2405.04015"]},"date_created":"2024-09-29T22:01:38Z","department":[{"_id":"KrCh"}],"author":[{"last_name":"Akshay","first_name":"S","full_name":"Akshay, S"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"publication_status":"published","publication":"Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence","date_published":"2024-09-01T00:00:00Z","ec_funded":1,"publisher":"International Joint Conferences on Artificial Intelligence","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.04015","open_access":"1"}],"abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a classical model for decision making in the presence of uncertainty. Often they are viewed as state transformers with planning objectives defned with respect to paths over MDP states. An increasingly\r\npopular alternative is to view them as distribution transformers, giving rise to a sequence of probability distributions over MDP states. For instance, reachability and safety properties in modeling robot swarms or chemical reaction networks are naturally defned in terms of probability distributions over states. Verifying such distributional properties is known to be hard and often beyond the reach of classical state-based verifcation techniques. In this work, we consider the problems of certifed policy (i.e. controller) verifcation and synthesis in MDPs under distributional reach-avoidance specifcations. By certifed we mean that, along with a policy, we also aim to synthesize a (checkable) certifcate ensuring that the MDP indeed satisfes the property. Thus, given the target set of distributions and an unsafe set of distributions over MDP states, our goal is to either synthesize a certifcate for a given policy or synthesize a policy along with a certifcate, proving that the target distribution can be reached while avoiding unsafe distributions. To solve this problem, we introduce the novel notion of distributional reach-avoid certifcates and present automated procedures for (1) synthesizing a certifcate for a given policy, and (2) synthesizing a policy together with the certifcate, both providing formal guarantees on certifcate correctness. Our experimental evaluation demonstrates the ability of our method to solve several non-trivial examples, including a multi-agent robot-swarm model, to synthesize certifed policies and to certify existing policies. "}],"language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"isbn":["9781956792041"],"issn":["1045-0823"]},"quality_controlled":"1","conference":{"start_date":"2024-08-03","location":"Jeju, Korea","end_date":"2024-08-09","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"doi":"10.24963/ijcai.2024/1","year":"2024","oa_version":"Preprint"},{"date_updated":"2025-04-14T07:52:46Z","oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Mehrdad Karrabi, Petr Novotný, and Dorde Zikelic. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” In <i>33rd International Joint Conference on Artificial Intelligence</i>, 6707–15. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>.","ama":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. Solving long-run average reward robust MDPs via stochastic games. In: <i>33rd International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:6707-6715. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>","apa":"Chatterjee, K., Goharshady, E., Karrabi, M., Novotný, P., &#38; Zikelic, D. (2024). Solving long-run average reward robust MDPs via stochastic games. In <i>33rd International Joint Conference on Artificial Intelligence</i> (pp. 6707–6715). Jeju, South Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>","mla":"Chatterjee, Krishnendu, et al. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” <i>33rd International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–15, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>.","ieee":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, and D. Zikelic, “Solving long-run average reward robust MDPs via stochastic games,” in <i>33rd International Joint Conference on Artificial Intelligence</i>, Jeju, South Korea, 2024, pp. 6707–6715.","short":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, D. Zikelic, in:, 33rd International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–6715.","ista":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. 2024. Solving long-run average reward robust MDPs via stochastic games. 33rd International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 6707–6715."},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"title":"Solving long-run average reward robust MDPs via stochastic games","OA_place":"repository","corr_author":"1","arxiv":1,"acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Czech Science Foundation\r\ngrant no. GA23-06963S.","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18160","scopus_import":"1","date_created":"2024-09-29T22:01:39Z","external_id":{"arxiv":["2312.13912"]},"department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Kafshdar Goharshadi, Ehsan","orcid":"0000-0002-8595-0587","first_name":"Ehsan","last_name":"Kafshdar Goharshadi","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d"},{"full_name":"Karrabi, Mehrdad","id":"67638922-f394-11eb-9cf6-f20423e08757","first_name":"Mehrdad","last_name":"Karrabi"},{"full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"publication_status":"published","page":"6707-6715","type":"conference","month":"09","status":"public","publisher":"International Joint Conferences on Artificial Intelligence","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.13912","open_access":"1"}],"abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) provide a standard framework for sequential decision making under uncertainty. However, MDPs do not take uncertainty in transition probabilities into account. Robust Markov decision processes (RMDPs) address this shortcoming of MDPs by assigning to each transition an uncertainty set rather than a single probability value. In this work, we consider polytopic RMDPs in which all uncertainty sets are polytopes and study the problem of solving long-run average reward polytopic RMDPs. We present a novel perspective on this problem and show that it can be reduced to solving long-run average reward turn-based stochastic games with finite state and action spaces. This reduction allows us to derive several important consequences that were hitherto not known to hold for polytopic RMDPs. First, we derive new computational complexity bounds for solving long-run average reward polytopic RMDPs, showing for the first time that the threshold decision problem for them is in NP∩CONP and that they admit a randomized algorithm with sub-exponential expected runtime. Second, we present Robust Polytopic Policy Iteration (RPPI), a novel policy iteration algorithm for solving long-run average reward polytopic RMDPs. Our experimental evaluation shows that RPPI is much more efficient in solving long-run average reward polytopic RMDPs compared to state-of-the-art methods based on value iteration. "}],"language":[{"iso":"eng"}],"article_processing_charge":"No","OA_type":"green","date_published":"2024-09-01T00:00:00Z","publication":"33rd International Joint Conference on Artificial Intelligence","ec_funded":1,"year":"2024","oa_version":"Preprint","publication_identifier":{"issn":["1045-0823"],"isbn":["9781956792041"]},"quality_controlled":"1","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2024-08-09","start_date":"2024-08-03","location":"Jeju, South Korea"},"doi":"10.24963/ijcai.2024/741"},{"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Holdase chaperones are essential in the mitochondrial membrane-protein biogenesis as they stabilize preproteins and keep them in an import-competent state as they travel through the aqueous cytosol and intermembrane space. The small TIM chaperones of the mitochondrial intermembrane space function within a fine balance of client promiscuity and high affinity binding, while being also able to release their client proteins without significant energy barrier to the downstream insertases/translocases. The tendency of the preproteins to aggregate and the dynamic nature of the preprotein—chaperone complexes makes the preparation of these complexes challenging. Here we present two optimized methods for complex formation of highly hydrophobic precursor proteins and chaperones: a pull-down approach and an in-vitro translation strategy. In the former, attaching the client protein to an affinity resin keeps the individual client protein copies apart from each other and decreases the client self-aggregation probability, thereby favouring complex formation. In the latter approach, a purified chaperone, added to the cell-free protein synthesis, captures the nascent precursor protein. The choice of method will depend on the desired client-chaperone complex amount, or the need for specific labeling scheme."}],"language":[{"iso":"eng"}],"article_processing_charge":"No","OA_type":"closed access","intvolume":"       707","publication":"Methods in Enzymology","date_published":"2024-09-13T00:00:00Z","volume":707,"year":"2024","oa_version":"None","publication_identifier":{"issn":["0076-6879"]},"quality_controlled":"1","doi":"10.1016/bs.mie.2024.07.051","date_updated":"2025-10-22T06:40:54Z","citation":{"ieee":"U. Guillerm, I. Sučec, and P. Schanda, “Generation of TIM chaperone substrate complexes,” in <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422.","mla":"Guillerm, Undina, et al. “Generation of TIM Chaperone Substrate Complexes.” <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422, doi:<a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">10.1016/bs.mie.2024.07.051</a>.","short":"U. Guillerm, I. Sučec, P. Schanda, in:, Methods in Enzymology, Elsevier, 2024, pp. 391–422.","ista":"Guillerm U, Sučec I, Schanda P. 2024.Generation of TIM chaperone substrate complexes. In: Methods in Enzymology. vol. 707, 391–422.","chicago":"Guillerm, Undina, Iva Sučec, and Paul Schanda. “Generation of TIM Chaperone Substrate Complexes.” In <i>Methods in Enzymology</i>, 707:391–422. Elsevier, 2024. <a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">https://doi.org/10.1016/bs.mie.2024.07.051</a>.","ama":"Guillerm U, Sučec I, Schanda P. Generation of TIM chaperone substrate complexes. In: <i>Methods in Enzymology</i>. Vol 707. Elsevier; 2024:391-422. doi:<a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">10.1016/bs.mie.2024.07.051</a>","apa":"Guillerm, U., Sučec, I., &#38; Schanda, P. (2024). Generation of TIM chaperone substrate complexes. In <i>Methods in Enzymology</i> (Vol. 707, pp. 391–422). Elsevier. <a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">https://doi.org/10.1016/bs.mie.2024.07.051</a>"},"title":"Generation of TIM chaperone substrate complexes","corr_author":"1","day":"13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18167","scopus_import":"1","external_id":{"pmid":["39488384"]},"date_created":"2024-10-01T10:58:27Z","department":[{"_id":"PaSc"}],"pmid":1,"author":[{"full_name":"Guillerm, Undina","first_name":"Undina","last_name":"Guillerm","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183"},{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"publication_status":"published","page":"391-422","type":"book_chapter","month":"09","status":"public"},{"publication":"Biomacromolecules","date_published":"2024-03-11T00:00:00Z","volume":25,"intvolume":"        25","abstract":[{"text":"Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film’s superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk.","lang":"eng"}],"publisher":"American Chemical Society","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1526-4602"],"issn":["1525-7797"]},"quality_controlled":"1","doi":"10.1021/acs.biomac.3c01239","has_accepted_license":"1","year":"2024","ddc":["540"],"oa_version":"Published Version","article_type":"original","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank Dr. Pavel Kielkowski for performing the MS/MS measurement and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro for introducing the Golden Gate Assembly technique in our lab. We acknowledge the support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB 1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie, and Universitätsgesellschaft München.","day":"11","scopus_import":"1","file_date_updated":"2024-10-07T08:33:35Z","_id":"18168","oa":1,"citation":{"ieee":"D. Wu <i>et al.</i>, “Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein,” <i>Biomacromolecules</i>, vol. 25, no. 3. American Chemical Society, pp. 1759–1774, 2024.","mla":"Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>, vol. 25, no. 3, American Chemical Society, 2024, pp. 1759–74, doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>.","short":"D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S. Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774.","ista":"Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 25(3), 1759–1774.","ama":"Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. 2024;25(3):1759-1774. doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>","chicago":"Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>.","apa":"Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D. C., Schneider, S., &#38; Rovo, P. (2024). Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>"},"date_updated":"2025-09-08T09:52:18Z","isi":1,"corr_author":"1","title":"Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein","page":"1759-1774","file":[{"creator":"dernst","file_size":6597227,"content_type":"application/pdf","success":1,"file_id":"18180","checksum":"9552b6d52f1e8a350764849a535fc13e","file_name":"2024_BioMacromolecules_Wu.pdf","date_updated":"2024-10-07T08:33:35Z","date_created":"2024-10-07T08:33:35Z","access_level":"open_access","relation":"main_file"}],"month":"03","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","department":[{"_id":"NMR"}],"external_id":{"pmid":["38343096"],"isi":["001166501000001"]},"date_created":"2024-10-02T10:09:53Z","publication_status":"published","author":[{"last_name":"Wu","first_name":"Dongqing","full_name":"Wu, Dongqing"},{"full_name":"Koscic, Anamaria","first_name":"Anamaria","last_name":"Koscic"},{"full_name":"Schneider, Sonja","last_name":"Schneider","first_name":"Sonja"},{"first_name":"Romeo C. A.","last_name":"Dubini","full_name":"Dubini, Romeo C. A."},{"last_name":"Rodriguez Camargo","first_name":"Diana C.","full_name":"Rodriguez Camargo, Diana C."},{"last_name":"Schneider","first_name":"Sabine","full_name":"Schneider, Sabine"},{"full_name":"Rovo, Petra","orcid":"0000-0001-8729-7326","first_name":"Petra","last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00"}],"pmid":1},{"year":"2024","oa_version":"None","article_type":"original","publication_identifier":{"eissn":["1096-0805"],"issn":["0022-2011"]},"doi":"10.1016/j.jip.2024.108209","quality_controlled":"1","abstract":[{"lang":"eng","text":"Defense against pathogens and parasites requires substantial investment of energy and resources on part of the host. This makes the host immune function dependent on availability and accessibility of resources. A resource deprived host is therefore expected to be more susceptible to infections, although empirical results do not always align with this prediction. Limiting host access to resources can additionally impact within-host pathogen numbers, either directly by altering the amount of resources available to the pathogens for proliferation or indirectly by altering the efficiency of the host immune system. We tested for the effects of host starvation (complete deprivation of resources) on susceptibility to bacterial pathogens, and within-host pathogen proliferation, in Drosophila melanogaster females. Our results show that starvation increases post-infection mortality of the host, but in a pathogen-specific manner. This increase in mortality is always accompanied by increased within-host pathogen proliferation. We therefore propose that starvation compromises host resistance to bacterial infections in Drosophila melanogaster females thereby increasing susceptibility to infections."}],"publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":207,"date_published":"2024-11-01T00:00:00Z","publication":"Journal of Invertebrate Pathology","intvolume":"       207","OA_type":"closed access","department":[{"_id":"SyCr"}],"external_id":{"pmid":["39322010"],"isi":["001327816900001"]},"date_created":"2024-10-06T22:01:11Z","publication_status":"published","author":[{"first_name":"Aabeer","last_name":"Basu","full_name":"Basu, Aabeer"},{"last_name":"Singh","first_name":"Aparajita","full_name":"Singh, Aparajita"},{"last_name":"Sehgal","first_name":"Suhaas","full_name":"Sehgal, Suhaas"},{"full_name":"Madaan, Tanvi","last_name":"Madaan","first_name":"Tanvi","id":"419917ac-5355-11ee-ae5a-c952babcaad9"},{"first_name":"Nagaraj Guru","last_name":"Prasad","full_name":"Prasad, Nagaraj Guru"}],"pmid":1,"month":"11","type":"journal_article","status":"public","citation":{"apa":"Basu, A., Singh, A., Sehgal, S., Madaan, T., &#38; Prasad, N. G. (2024). Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. <i>Journal of Invertebrate Pathology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jip.2024.108209\">https://doi.org/10.1016/j.jip.2024.108209</a>","ama":"Basu A, Singh A, Sehgal S, Madaan T, Prasad NG. Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. <i>Journal of Invertebrate Pathology</i>. 2024;207(11). doi:<a href=\"https://doi.org/10.1016/j.jip.2024.108209\">10.1016/j.jip.2024.108209</a>","chicago":"Basu, Aabeer, Aparajita Singh, Suhaas Sehgal, Tanvi Madaan, and Nagaraj Guru Prasad. “Starvation Increases Susceptibility to Bacterial Infection and Promotes Systemic Pathogen Proliferation in Drosophila Melanogaster Females.” <i>Journal of Invertebrate Pathology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jip.2024.108209\">https://doi.org/10.1016/j.jip.2024.108209</a>.","short":"A. Basu, A. Singh, S. Sehgal, T. Madaan, N.G. Prasad, Journal of Invertebrate Pathology 207 (2024).","ista":"Basu A, Singh A, Sehgal S, Madaan T, Prasad NG. 2024. Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females. Journal of Invertebrate Pathology. 207(11), 108209.","mla":"Basu, Aabeer, et al. “Starvation Increases Susceptibility to Bacterial Infection and Promotes Systemic Pathogen Proliferation in Drosophila Melanogaster Females.” <i>Journal of Invertebrate Pathology</i>, vol. 207, no. 11, 108209, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jip.2024.108209\">10.1016/j.jip.2024.108209</a>.","ieee":"A. Basu, A. Singh, S. Sehgal, T. Madaan, and N. G. Prasad, “Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females,” <i>Journal of Invertebrate Pathology</i>, vol. 207, no. 11. Elsevier, 2024."},"date_updated":"2025-09-08T09:53:50Z","isi":1,"corr_author":"1","title":"Starvation increases susceptibility to bacterial infection and promotes systemic pathogen proliferation in Drosophila melanogaster females","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"11","day":"01","article_number":"108209","acknowledgement":"The authors thank Tejashwini Hegde for logistical support during execution of the experiments reported here. The authors thank Prof. P. Cornelis (Vrije Universiteit Brussel, Belgium) for providing the Pseudomonas entomophila isolate, Dr. Elio Sucena and Tania Paulo (Instituto Gulbenkian Ciencia, Portugal) for providing the Erwinia c. carotovora, and Prof. Brian Lazzaro (Cornell University, USA) for providing the Enterococcus faecalis and Providencia rettgeri isolates, and Dr. Karan Singh (IISER Mohali, India) for isolating the Staphylococcus succinus isolate used in the experiments. The authors also thank Dr. Manas Geeta Arun for maintenance of the LH fly populations used in this study.\r\nThe study was funded by intra-mural funding from IISER Mohali, India, to NGP. AB was supported by Senior Research Fellowship for PhD students from CSIR, Govt. of India. AS was supported by Senior Research Fellowship for PhD students from UGC, Govt. of India. SS and TM were supported by KVPY fellowships for undergraduate studies from DST, Govt. of India.","scopus_import":"1","_id":"18171"},{"year":"2024","oa_version":"Published Version","ddc":["520"],"article_type":"original","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"quality_controlled":"1","doi":"10.1093/mnras/stae2053","has_accepted_license":"1","abstract":[{"text":"Red Giant stars host solar-like oscillations which have mixed character, being sensitive to conditions both in the outer convection zone and deep within the interior. The properties of these modes are sensitive to both core rotation and magnetic fields. While asteroseismic studies of the former have been done on a large scale, studies of the latter are currently limited to tens of stars. We aim to produce the first large catalogue of both magnetic and rotational perturbations. We jointly constrain these parameters by devising an automated method for fitting the power spectra directly. We successfully apply the method to 302 low-luminosity red giants. We find a clear bimodality in core rotation rate. The primary peak is at δνrot = 0.32 μHz, and the secondary at δνrot = 0.47 μHz. Combining our results with literature values, we find that the percentage of stars rotating much more rapidly than the population average increases with evolutionary state. We measure magnetic splittings of 2σ significance in 23 stars. While the most extreme magnetic splitting values appear in stars with masses > 1.1M⊙, implying they formerly hosted a convective core, a small but statistically significant magnetic splitting is measured at lower masses. Asymmetry between the frequencies of a rotationally split multiplet has previously been used to diagnose the presence of a magnetic perturbation. We find that of the stars with a significant detection of magnetic perturbation, 43\\% do not show strong asymmetry. We find no strong evidence of correlation between the rotation and magnetic parameters.","lang":"eng"}],"publisher":"Oxford University Press","language":[{"iso":"eng"}],"DOAJ_listed":"1","article_processing_charge":"Yes","date_published":"2024-10-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","volume":534,"OA_type":"gold","intvolume":"       534","department":[{"_id":"LiBu"}],"external_id":{"arxiv":["2409.01157"],"isi":["001320536900011"]},"date_created":"2024-10-06T22:01:11Z","publication_status":"published","author":[{"last_name":"Hatt","first_name":"Emily J.","full_name":"Hatt, Emily J."},{"last_name":"Ong","first_name":"J. M.Joel","full_name":"Ong, J. M.Joel"},{"full_name":"Nielsen, Martin B.","first_name":"Martin B.","last_name":"Nielsen"},{"full_name":"Chaplin, William J.","first_name":"William J.","last_name":"Chaplin"},{"full_name":"Davies, Guy R.","first_name":"Guy R.","last_name":"Davies"},{"last_name":"Deheuvels","first_name":"Sébastien","full_name":"Deheuvels, Sébastien"},{"full_name":"Ballot, Jérôme","first_name":"Jérôme","last_name":"Ballot"},{"full_name":"Li, Gang","last_name":"Li","first_name":"Gang"},{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501"}],"file":[{"file_name":"2024_MonthlyNRoyalAstronSoc_Hatt.pdf","date_created":"2024-10-07T09:14:03Z","date_updated":"2024-10-07T09:14:03Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_size":2813008,"content_type":"application/pdf","checksum":"b79f3c6a5991516abbcc8d34fa4bfb5f","success":1,"file_id":"18182"}],"page":"1060-1076","month":"10","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","oa":1,"citation":{"mla":"Hatt, Emily J., et al. “Asteroseismic Signatures of Core Magnetism and Rotation in Hundreds of Low-Luminosity Red Giants.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 2, Oxford University Press, 2024, pp. 1060–76, doi:<a href=\"https://doi.org/10.1093/mnras/stae2053\">10.1093/mnras/stae2053</a>.","ieee":"E. J. Hatt <i>et al.</i>, “Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 534, no. 2. Oxford University Press, pp. 1060–1076, 2024.","short":"E.J. Hatt, J.M.J. Ong, M.B. Nielsen, W.J. Chaplin, G.R. Davies, S. Deheuvels, J. Ballot, G. Li, L.A. Bugnet, Monthly Notices of the Royal Astronomical Society 534 (2024) 1060–1076.","ista":"Hatt EJ, Ong JMJ, Nielsen MB, Chaplin WJ, Davies GR, Deheuvels S, Ballot J, Li G, Bugnet LA. 2024. Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. Monthly Notices of the Royal Astronomical Society. 534(2), 1060–1076.","chicago":"Hatt, Emily J., J. M.Joel Ong, Martin B. Nielsen, William J. Chaplin, Guy R. Davies, Sébastien Deheuvels, Jérôme Ballot, Gang Li, and Lisa Annabelle Bugnet. “Asteroseismic Signatures of Core Magnetism and Rotation in Hundreds of Low-Luminosity Red Giants.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stae2053\">https://doi.org/10.1093/mnras/stae2053</a>.","ama":"Hatt EJ, Ong JMJ, Nielsen MB, et al. Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;534(2):1060-1076. doi:<a href=\"https://doi.org/10.1093/mnras/stae2053\">10.1093/mnras/stae2053</a>","apa":"Hatt, E. J., Ong, J. M. J., Nielsen, M. B., Chaplin, W. J., Davies, G. R., Deheuvels, S., … Bugnet, L. A. (2024). Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stae2053\">https://doi.org/10.1093/mnras/stae2053</a>"},"PlanS_conform":"1","date_updated":"2025-09-08T09:53:01Z","isi":1,"arxiv":1,"title":"Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants","OA_place":"publisher","issue":"2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"EJH, WJC, and GRD acknowledge the support of Science and Technology Facilities Council. MBN acknowledges support from the UK Space Agency. JMJO acknowledges support from NASA through the NASA Hubble Fellowship grant HST-HF2-51517.001, awarded by STScI (Space Telescope Science Institute), which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The authors acknowledge use of the Blue-BEAR HPC service at the University of Birmingham. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission was provided by the NASA Science Mission Directorate. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/web/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC was provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This paper received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (CartographY GA. 804752). SD and JB acknowledge support from the Centre National d’Etudes Spatiales (CNES).","day":"01","file_date_updated":"2024-10-07T09:14:03Z","scopus_import":"1","_id":"18172"},{"oa":1,"citation":{"apa":"Wassermair, M., Kahl, G., Roth, R., &#38; Archer, A. J. (2024). Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>","chicago":"Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0226954\">https://doi.org/10.1063/5.0226954</a>.","ama":"Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. <i>The Journal of chemical physics</i>. 2024;161(12). doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>","ista":"Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 161(12), 124503.","short":"M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics 161 (2024).","ieee":"M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system,” <i>The Journal of chemical physics</i>, vol. 161, no. 12. AIP Publishing, 2024.","mla":"Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” <i>The Journal of Chemical Physics</i>, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0226954\">10.1063/5.0226954</a>."},"date_updated":"2025-09-08T09:55:52Z","arxiv":1,"corr_author":"1","isi":1,"title":"Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"12","day":"28","article_number":"124503 ","acknowledgement":"The computational results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1.","file_date_updated":"2024-10-07T11:25:00Z","scopus_import":"1","_id":"18174","department":[{"_id":"GradSch"}],"date_created":"2024-10-06T22:01:12Z","external_id":{"arxiv":["2409.06447"],"isi":["001325268300004"],"pmid":["39344889"]},"publication_status":"published","author":[{"full_name":"Wassermair, Michael","last_name":"Wassermair","first_name":"Michael","id":"23d132c4-4e98-11ef-b275-9e8d4cd8c917"},{"first_name":"Gerhard","last_name":"Kahl","full_name":"Kahl, Gerhard"},{"first_name":"Roland","last_name":"Roth","full_name":"Roth, Roland"},{"first_name":"Andrew J.","last_name":"Archer","full_name":"Archer, Andrew J."}],"pmid":1,"month":"09","type":"journal_article","file":[{"success":1,"checksum":"f3874e64ef94e94b2376f00a1fee24c3","file_id":"18185","content_type":"application/pdf","file_size":15009000,"creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2024-10-07T11:25:00Z","date_created":"2024-10-07T11:25:00Z","file_name":"2024_JourChemicalPhysics_Wassermair.pdf"}],"status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise."}],"publisher":"AIP Publishing","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"volume":161,"date_published":"2024-09-28T00:00:00Z","publication":"The Journal of chemical physics","intvolume":"       161","year":"2024","oa_version":"Published Version","ddc":["530"],"article_type":"original","publication_identifier":{"eissn":["1089-7690"]},"doi":"10.1063/5.0226954","quality_controlled":"1","has_accepted_license":"1"},{"volume":313,"date_published":"2024-09-01T00:00:00Z","publication":"38th European Conference on Object-Oriented Programming","intvolume":"       313","abstract":[{"text":"Large-scale software repositories are a source of insights for software engineering. They offer an unmatched window into the software development process at scale. Their sheer number and size holds the promise of broadly applicable results. At the same time, that very size presents practical challenges for scaling tools and algorithms to millions of projects. A reasonable approach is to limit studies to representative samples of the population of interest. Broadly applicable conclusions can then be obtained by generalizing to the entire population. The contribution of this paper is a standardized experimental design methodology for choosing the inputs of studies working with large-scale repositories. We advocate for a methodology that clearly lays out what the population of interest is, how to sample it, and that fosters reproducibility. Along the way, we discourage researchers from using extrinsic attributes of projects such as stars, that measure some unclear notion of popularity.","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773416"]},"conference":{"name":"ECOOP: European Conference on Object-Oriented Programming","end_date":"2024-09-20","start_date":"2024-09-16","location":"Vienna, Austria"},"doi":"10.4230/LIPIcs.ECOOP.2024.27","quality_controlled":"1","has_accepted_license":"1","year":"2024","ddc":["000"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"27","day":"01","acknowledgement":"This work was supported by the Czech Ministry of Education, Youth and Sports under\r\nprogram ERC-CZ, grant agreement LL2325, BigCode (reg. no. CZ.02.1.01/0.0/0.0/15_003/0000421). NSF grants CCF-1910850, CNS-1925644, and CCF-2139612, as well as the GACR EXPRO grant 23-07580X. We would like to thank Digital Ocean for their involuntary contribution of computational resources during the early data gathering phase of our research. We acknoweldge the reviewers of ICSE’22, and thank the reviewers of ECOOP’23 for their encouragments and for sticking around until 2024.","file_date_updated":"2024-10-07T11:10:55Z","scopus_import":"1","_id":"18175","oa":1,"citation":{"chicago":"Maj, Petr, Stefanie Muroya Lei, Konrad Siek, Luca Di Grazia, and Jan Vitek. “The Fault in Our Stars: Designing Reproducible Large-Scale Code Analysis Experiments.” In <i>38th European Conference on Object-Oriented Programming</i>, Vol. 313. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">https://doi.org/10.4230/LIPIcs.ECOOP.2024.27</a>.","ama":"Maj P, Muroya Lei S, Siek K, Di Grazia L, Vitek J. The fault in our stars: Designing reproducible large-scale code analysis experiments. In: <i>38th European Conference on Object-Oriented Programming</i>. Vol 313. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">10.4230/LIPIcs.ECOOP.2024.27</a>","apa":"Maj, P., Muroya Lei, S., Siek, K., Di Grazia, L., &#38; Vitek, J. (2024). The fault in our stars: Designing reproducible large-scale code analysis experiments. In <i>38th European Conference on Object-Oriented Programming</i> (Vol. 313). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">https://doi.org/10.4230/LIPIcs.ECOOP.2024.27</a>","mla":"Maj, Petr, et al. “The Fault in Our Stars: Designing Reproducible Large-Scale Code Analysis Experiments.” <i>38th European Conference on Object-Oriented Programming</i>, vol. 313, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ECOOP.2024.27\">10.4230/LIPIcs.ECOOP.2024.27</a>.","ieee":"P. Maj, S. Muroya Lei, K. Siek, L. Di Grazia, and J. Vitek, “The fault in our stars: Designing reproducible large-scale code analysis experiments,” in <i>38th European Conference on Object-Oriented Programming</i>, Vienna, Austria, 2024, vol. 313.","ista":"Maj P, Muroya Lei S, Siek K, Di Grazia L, Vitek J. 2024. The fault in our stars: Designing reproducible large-scale code analysis experiments. 38th European Conference on Object-Oriented Programming. ECOOP: European Conference on Object-Oriented Programming, LIPIcs, vol. 313, 27.","short":"P. Maj, S. Muroya Lei, K. Siek, L. Di Grazia, J. Vitek, in:, 38th European Conference on Object-Oriented Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024."},"date_updated":"2025-12-02T13:48:19Z","isi":1,"title":"The fault in our stars: Designing reproducible large-scale code analysis experiments","alternative_title":["LIPIcs"],"type":"conference","month":"09","file":[{"creator":"dernst","file_size":1764222,"content_type":"application/pdf","success":1,"file_id":"18184","checksum":"2e75d305a8c817d76a0c7f136ce34f86","file_name":"2024_LIPICs_Maj.pdf","date_created":"2024-10-07T11:10:55Z","date_updated":"2024-10-07T11:10:55Z","access_level":"open_access","relation":"main_file"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","department":[{"_id":"ToHe"}],"external_id":{"isi":["001533999700027"]},"date_created":"2024-10-06T22:01:12Z","publication_status":"published","author":[{"full_name":"Maj, Petr","first_name":"Petr","last_name":"Maj"},{"full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff"},{"full_name":"Siek, Konrad","last_name":"Siek","first_name":"Konrad"},{"last_name":"Di Grazia","first_name":"Luca","full_name":"Di Grazia, Luca"},{"full_name":"Vitek, Jan","first_name":"Jan","last_name":"Vitek"}]},{"year":"2024","ddc":["530"],"oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["2691-3399"]},"quality_controlled":"1","doi":"10.1103/PRXQuantum.5.030356","has_accepted_license":"1","abstract":[{"text":"Introducing a class of SU(2) invariant quantum unitary circuits generating chiral transport, we examine the role of broken space-reflection and time-reversal symmetries on spin-transport properties. Upon adjusting parameters of local unitary gates, the dynamics can be either chaotic or integrable. The latter corresponds to a generalization of the space-time discretized (Trotterized) higher-spin quantum Heisenberg chain. We demonstrate that breaking of space-reflection symmetry results in a drift in the dynamical spin susceptibility. Remarkably, we find a universal drift velocity given by a simple formula, which, at zero average magnetization, depends only on the values of SU(2) Casimir invariants associated with local spins. In the integrable case, the drift velocity formula is confirmed analytically based on the exact solution of thermodynamic Bethe ansatz equations. Finally, by inspecting the large fluctuations of the time-integrated current between two halves of the system in stationary maximum-entropy states, we demonstrate violation of the Gallavotti-Cohen symmetry, implying that such states cannot be regarded as equilibrium ones. We show that the scaled cumulant generating function of the time-integrated current instead obeys a generalized fluctuation relation.","lang":"eng"}],"publisher":"American Physical Society","DOAJ_listed":"1","language":[{"iso":"eng"}],"article_processing_charge":"Yes","publication":"PRX Quantum","date_published":"2024-09-25T00:00:00Z","ec_funded":1,"volume":5,"OA_type":"gold","intvolume":"         5","department":[{"_id":"MaSe"}],"date_created":"2024-10-06T22:01:12Z","external_id":{"arxiv":["2406.01571"],"isi":["001327172800001"]},"publication_status":"published","author":[{"full_name":"Zadnik, Lenart","last_name":"Zadnik","first_name":"Lenart"},{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko"},{"full_name":"Krajnik, Žiga","last_name":"Krajnik","first_name":"Žiga"},{"full_name":"Ilievski, Enej","first_name":"Enej","last_name":"Ilievski"},{"last_name":"Prosen","first_name":"Tomaž","full_name":"Prosen, Tomaž"}],"file":[{"content_type":"application/pdf","file_size":1061648,"checksum":"bc230631255d3bcf8bcbbc8fdbfefcf2","success":1,"file_id":"18183","creator":"dernst","date_updated":"2024-10-07T11:04:12Z","date_created":"2024-10-07T11:04:12Z","file_name":"2024_PRXQuantum_Zadnik.pdf","relation":"main_file","access_level":"open_access"}],"month":"09","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"apa":"Zadnik, L., Ljubotina, M., Krajnik, Ž., Ilievski, E., &#38; Prosen, T. (2024). Quantum many-body spin ratchets. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>","ama":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. Quantum many-body spin ratchets. <i>PRX Quantum</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>","chicago":"Zadnik, Lenart, Marko Ljubotina, Žiga Krajnik, Enej Ilievski, and Tomaž Prosen. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">https://doi.org/10.1103/PRXQuantum.5.030356</a>.","ista":"Zadnik L, Ljubotina M, Krajnik Ž, Ilievski E, Prosen T. 2024. Quantum many-body spin ratchets. PRX Quantum. 5(3), 030356.","short":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, T. Prosen, PRX Quantum 5 (2024).","mla":"Zadnik, Lenart, et al. “Quantum Many-Body Spin Ratchets.” <i>PRX Quantum</i>, vol. 5, no. 3, 030356, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.5.030356\">10.1103/PRXQuantum.5.030356</a>.","ieee":"L. Zadnik, M. Ljubotina, Ž. Krajnik, E. Ilievski, and T. Prosen, “Quantum many-body spin ratchets,” <i>PRX Quantum</i>, vol. 5, no. 3. American Physical Society, 2024."},"oa":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"date_updated":"2025-09-08T09:55:09Z","isi":1,"arxiv":1,"title":"Quantum many-body spin ratchets","OA_place":"publisher","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"The authors thank Denis Bernard, Jérôme Dubail, Hosho Katsura, Kareljan Schoutens, and Alberto Zorzato for stimulating discussions. This work has been supported by: Slovenian Research Agency (ARIS) under Grants No. N1-0219 (T.P., L.Z.), No. N1-0334 (T.P., L.Z.), No. N1-0243 (E.I.), and under Research Program P1-0402 (E.I., T.P., L.Z.). European Research Council (ERC) under Consolidator Grant No. 771536—NEMO (L.Z.), Advanced Grant No.\r\n101096208—QUEST (T.P., L.Z.), and Starting Grant No. 850899—NEQuM (M.L.). Simons Foundation under Simons Junior Fellowship Grant No. 1141511 (Ž.K.). M.L. acknowledges the hospitality of the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-2210452. Numerical simulations were performed using the ITensor library [117]. ","day":"25","article_number":"030356","file_date_updated":"2024-10-07T11:04:12Z","scopus_import":"1","_id":"18176"},{"date_created":"2024-10-06T22:01:12Z","external_id":{"isi":["001333144400002"]},"department":[{"_id":"ToHe"}],"author":[{"full_name":"Beneš, Nikola","first_name":"Nikola","last_name":"Beneš"},{"full_name":"Brim, Luboš","last_name":"Brim","first_name":"Luboš"},{"first_name":"Ondřej","last_name":"Huvar","full_name":"Huvar, Ondřej"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","first_name":"Samuel","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"},{"last_name":"Šafránek","first_name":"David","full_name":"Šafránek, David"}],"publication_status":"published","month":"09","type":"conference","page":"19-26","alternative_title":["LNBI"],"status":"public","date_updated":"2025-09-08T09:54:27Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"citation":{"ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2024. BNClassifier: Classifying boolean models by dynamic properties. Computational Methods in Systems Biology. , LNBI, vol. 14971, 19–26.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, in:, Computational Methods in Systems Biology, Springer Nature, 2024, pp. 19–26.","mla":"Beneš, Nikola, et al. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” <i>Computational Methods in Systems Biology</i>, vol. 14971, Springer Nature, 2024, pp. 19–26, doi:<a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">10.1007/978-3-031-71671-3_2</a>.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “BNClassifier: Classifying boolean models by dynamic properties,” in <i>Computational Methods in Systems Biology</i>, 2024, vol. 14971, pp. 19–26.","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2024). BNClassifier: Classifying boolean models by dynamic properties. In <i>Computational Methods in Systems Biology</i> (Vol. 14971, pp. 19–26). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">https://doi.org/10.1007/978-3-031-71671-3_2</a>","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” In <i>Computational Methods in Systems Biology</i>, 14971:19–26. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">https://doi.org/10.1007/978-3-031-71671-3_2</a>.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. BNClassifier: Classifying boolean models by dynamic properties. In: <i>Computational Methods in Systems Biology</i>. Vol 14971. Springer Nature; 2024:19-26. doi:<a href=\"https://doi.org/10.1007/978-3-031-71671-3_2\">10.1007/978-3-031-71671-3_2</a>"},"title":"BNClassifier: Classifying boolean models by dynamic properties","isi":1,"day":"19","acknowledgement":"The work has been supported by the Czech Science Foundation grant No. GA22-10845S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18177","scopus_import":"1","year":"2024","oa_version":"None","publication_identifier":{"isbn":["9783031716706"],"issn":["0302-9743"],"eissn":["1611-3349"]},"doi":"10.1007/978-3-031-71671-3_2","quality_controlled":"1","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Partially Specified Boolean Networks (PSBNs) represent a family of Boolean models resulting from possible interpretations of unknown update logics. Hybrid extension of CTL (HCTL) has the power to express complex dynamical phenomena, such as oscillations or stability. We present BNClassifier to classify Boolean Networks corresponding to a given PSBN according to criteria specified in HCTL. The implementation of the tool is fully symbolic (based on BDDs). The results are visualised using the machine-learning-based technology of decision trees."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"intvolume":"     14971","ec_funded":1,"volume":14971,"date_published":"2024-09-19T00:00:00Z","publication":"Computational Methods in Systems Biology"},{"intvolume":"        20","day":"19","volume":20,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Physics","date_published":"2024-01-19T00:00:00Z","issue":"3","_id":"18187","scopus_import":"1","date_updated":"2024-10-14T07:54:20Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Quasicrystals are ordered but not periodic, which makes them fascinating objects at the interface between order and disorder. Experiments with ultracold atoms zoom in on this interface by driving a quasicrystal and exploring its fractal properties."}],"citation":{"mla":"Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>, vol. 20, no. 3, Springer Nature, 2024, pp. 351–52, doi:<a href=\"https://doi.org/10.1038/s41567-023-02357-0\">10.1038/s41567-023-02357-0</a>.","ieee":"J. Leonard, “A kicked quasicrystal,” <i>Nature Physics</i>, vol. 20, no. 3. Springer Nature, pp. 351–352, 2024.","short":"J. Leonard, Nature Physics 20 (2024) 351–352.","ista":"Leonard J. 2024. A kicked quasicrystal. Nature Physics. 20(3), 351–352.","ama":"Leonard J. A kicked quasicrystal. <i>Nature Physics</i>. 2024;20(3):351-352. doi:<a href=\"https://doi.org/10.1038/s41567-023-02357-0\">10.1038/s41567-023-02357-0</a>","chicago":"Leonard, Julian. “A Kicked Quasicrystal.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-023-02357-0\">https://doi.org/10.1038/s41567-023-02357-0</a>.","apa":"Leonard, J. (2024). A kicked quasicrystal. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02357-0\">https://doi.org/10.1038/s41567-023-02357-0</a>"},"article_processing_charge":"No","language":[{"iso":"eng"}],"title":"A kicked quasicrystal","type":"journal_article","month":"01","page":"351-352","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"status":"public","doi":"10.1038/s41567-023-02357-0","quality_controlled":"1","date_created":"2024-10-07T11:45:17Z","year":"2024","extern":"1","author":[{"id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","orcid":"0000-0003-3696-6870","first_name":"Julian","last_name":"Leonard","full_name":"Leonard, Julian"}],"article_type":"letter_note","publication_status":"published","oa_version":"None"},{"day":"27","article_number":"1388","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18188","scopus_import":"1","date_updated":"2024-10-08T11:15:55Z","oa":1,"citation":{"ista":"Blatz T, Kwan J, Leonard J, Bohrdt A. 2024. Bayesian optimization for robust state preparation in quantum many-body systems. Quantum. 8, 1388.","short":"T. Blatz, J. Kwan, J. Leonard, A. Bohrdt, Quantum 8 (2024).","ieee":"T. Blatz, J. Kwan, J. Leonard, and A. Bohrdt, “Bayesian optimization for robust state preparation in quantum many-body systems,” <i>Quantum</i>, vol. 8. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024.","mla":"Blatz, Tizian, et al. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” <i>Quantum</i>, vol. 8, 1388, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024, doi:<a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">10.22331/q-2024-06-27-1388</a>.","apa":"Blatz, T., Kwan, J., Leonard, J., &#38; Bohrdt, A. (2024). Bayesian optimization for robust state preparation in quantum many-body systems. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">https://doi.org/10.22331/q-2024-06-27-1388</a>","chicago":"Blatz, Tizian, Joyce Kwan, Julian Leonard, and Annabelle Bohrdt. “Bayesian Optimization for Robust State Preparation in Quantum Many-Body Systems.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2024. <a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">https://doi.org/10.22331/q-2024-06-27-1388</a>.","ama":"Blatz T, Kwan J, Leonard J, Bohrdt A. Bayesian optimization for robust state preparation in quantum many-body systems. <i>Quantum</i>. 2024;8. doi:<a href=\"https://doi.org/10.22331/q-2024-06-27-1388\">10.22331/q-2024-06-27-1388</a>"},"title":"Bayesian optimization for robust state preparation in quantum many-body systems","arxiv":1,"month":"06","type":"journal_article","status":"public","date_created":"2024-10-07T11:45:56Z","external_id":{"arxiv":["2312.09253"]},"extern":"1","author":[{"last_name":"Blatz","first_name":"Tizian","full_name":"Blatz, Tizian"},{"full_name":"Kwan, Joyce","last_name":"Kwan","first_name":"Joyce"},{"first_name":"Julian","last_name":"Leonard","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","full_name":"Leonard, Julian"},{"full_name":"Bohrdt, Annabelle","first_name":"Annabelle","last_name":"Bohrdt"}],"publication_status":"published","intvolume":"         8","volume":8,"date_published":"2024-06-27T00:00:00Z","publication":"Quantum","main_file_link":[{"open_access":"1","url":"https://doi.org/10.22331/q-2024-06-27-1388"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","abstract":[{"lang":"eng","text":"New generations of ultracold-atom experiments are continually raising the demand for efficient solutions to optimal control problems. Here, we apply Bayesian optimization to improve a state-preparation protocol recently implemented in an ultracold-atom system to realize a two-particle fractional quantum Hall state. Compared to manual ramp design, we demonstrate the superior performance of our optimization approach in a numerical simulation – resulting in a protocol that is 10x faster at the same fidelity, even when taking into account experimentally realistic levels of disorder in the system. We extensively analyze and discuss questions of robustness and the relationship between numerical simulation and experimental realization, and how to make the best use of the surrogate model trained during optimization. We find that numerical simulation can be expected to substantially reduce the number of experiments that need to be performed with even the most basic transfer learning techniques. The proposed protocol and workflow will pave the way toward the realization of more complex many-body quantum states in experiments."}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2521-327X"]},"doi":"10.22331/q-2024-06-27-1388","quality_controlled":"1","year":"2024","article_type":"original","oa_version":"Published Version"},{"date_published":"2024-04-11T00:00:00Z","publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2404.07481","day":"11","_id":"18202","oa":1,"citation":{"apa":"Kim, S., Lukin, A., Rispoli, M., Tai, M. E., Kaufman, A. M., Segura, P., … Greiner, M. (n.d.). Adiabatic state preparation in a quantum Ising spin chain. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2404.07481\">https://doi.org/10.48550/arXiv.2404.07481</a>","ama":"Kim S, Lukin A, Rispoli M, et al. Adiabatic state preparation in a quantum Ising spin chain. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2404.07481\">10.48550/arXiv.2404.07481</a>","chicago":"Kim, Sooshin, Alexander Lukin, Matthew Rispoli, M. Eric Tai, Adam M. Kaufman, Perrin Segura, Yanfei Li, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2404.07481\">https://doi.org/10.48550/arXiv.2404.07481</a>.","ista":"Kim S, Lukin A, Rispoli M, Tai ME, Kaufman AM, Segura P, Li Y, Kwan J, Leonard J, Brice Bakkali-Hassani BB-H, Greiner M. Adiabatic state preparation in a quantum Ising spin chain. arXiv, 2404.07481.","short":"S. Kim, A. Lukin, M. Rispoli, M.E. Tai, A.M. Kaufman, P. Segura, Y. Li, J. Kwan, J. Leonard, B.B.-H. Brice Bakkali-Hassani, M. Greiner, ArXiv (n.d.).","ieee":"S. Kim <i>et al.</i>, “Adiabatic state preparation in a quantum Ising spin chain,” <i>arXiv</i>. .","mla":"Kim, Sooshin, et al. “Adiabatic State Preparation in a Quantum Ising Spin Chain.” <i>ArXiv</i>, 2404.07481, doi:<a href=\"https://doi.org/10.48550/arXiv.2404.07481\">10.48550/arXiv.2404.07481</a>."},"abstract":[{"lang":"eng","text":"We report on adiabatic state preparation in the one-dimensional quantum Ising\r\nmodel using ultracold bosons in a tilted optical lattice. We prepare many-body\r\nground states of controllable system sizes and observe enhanced fluctuations\r\naround the transition between paramagnetic and antiferromagnetic states,\r\nmarking the precursor of quantum critical behavior. Furthermore, we find\r\nevidence for superpositions of domain walls and study their effect on the\r\nmany-body ground state by measuring the populations of each spin configuration\r\nacross the transition. These results shed new light on the effect of boundary\r\nconditions in finite-size quantum systems."}],"date_updated":"2024-10-08T11:28:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.07481"}],"arxiv":1,"language":[{"iso":"eng"}],"title":"Adiabatic state preparation in a quantum Ising spin chain","article_processing_charge":"No","type":"preprint","month":"04","doi":"10.48550/arXiv.2404.07481","status":"public","extern":"1","year":"2024","external_id":{"arxiv":["2404.07481"]},"date_created":"2024-10-08T11:25:52Z","oa_version":"Preprint","publication_status":"submitted","author":[{"full_name":"Kim, Sooshin","first_name":"Sooshin","last_name":"Kim"},{"full_name":"Lukin, Alexander","first_name":"Alexander","last_name":"Lukin"},{"full_name":"Rispoli, Matthew","first_name":"Matthew","last_name":"Rispoli"},{"full_name":"Tai, M. Eric","first_name":"M. Eric","last_name":"Tai"},{"first_name":"Adam M.","last_name":"Kaufman","full_name":"Kaufman, Adam M."},{"first_name":"Perrin","last_name":"Segura","full_name":"Segura, Perrin"},{"full_name":"Li, Yanfei","first_name":"Yanfei","last_name":"Li"},{"first_name":"Joyce","last_name":"Kwan","full_name":"Kwan, Joyce"},{"full_name":"Leonard, Julian","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","first_name":"Julian","last_name":"Leonard"},{"last_name":"Brice Bakkali-Hassani","first_name":"Brice Bakkali-Hassani","full_name":"Brice Bakkali-Hassani, Brice Bakkali-Hassani"},{"full_name":"Greiner, Markus","first_name":"Markus","last_name":"Greiner"}]},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","month":"07","type":"journal_article","author":[{"first_name":"Aviv A.","last_name":"Rosenberg","full_name":"Rosenberg, Aviv A."},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein"}],"pmid":1,"publication_status":"published","external_id":{"pmid":["39019896"]},"date_created":"2024-10-08T11:50:30Z","extern":"1","_id":"18203","scopus_import":"1","day":"17","article_number":"783","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A dataset of alternately located segments in protein crystal structures","date_updated":"2024-10-09T10:08:08Z","oa":1,"citation":{"short":"A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Data 11 (2024).","ista":"Rosenberg AA, Marx A, Bronstein AM. 2024. A dataset of alternately located segments in protein crystal structures. Scientific Data. 11, 783.","mla":"Rosenberg, Aviv A., et al. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” <i>Scientific Data</i>, vol. 11, 783, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41597-024-03595-4\">10.1038/s41597-024-03595-4</a>.","ieee":"A. A. Rosenberg, A. Marx, and A. M. Bronstein, “A dataset of alternately located segments in protein crystal structures,” <i>Scientific Data</i>, vol. 11. Springer Nature, 2024.","apa":"Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2024). A dataset of alternately located segments in protein crystal structures. <i>Scientific Data</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41597-024-03595-4\">https://doi.org/10.1038/s41597-024-03595-4</a>","chicago":"Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “A Dataset of Alternately Located Segments in Protein Crystal Structures.” <i>Scientific Data</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41597-024-03595-4\">https://doi.org/10.1038/s41597-024-03595-4</a>.","ama":"Rosenberg AA, Marx A, Bronstein AM. A dataset of alternately located segments in protein crystal structures. <i>Scientific Data</i>. 2024;11. doi:<a href=\"https://doi.org/10.1038/s41597-024-03595-4\">10.1038/s41597-024-03595-4</a>"},"has_accepted_license":"1","doi":"10.1038/s41597-024-03595-4","quality_controlled":"1","publication_identifier":{"issn":["2052-4463"]},"article_type":"original","oa_version":"Published Version","year":"2024","intvolume":"        11","volume":11,"publication":"Scientific Data","date_published":"2024-07-17T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41597-024-03595-4","open_access":"1"}],"publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function."}]},{"scopus_import":"1","_id":"18204","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"141","day":"01","title":"Data-driven modeling of interrelated dynamical systems","citation":{"short":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, A.M. Bronstein, Communications Physics 7 (2024).","ista":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. 2024. Data-driven modeling of interrelated dynamical systems. Communications Physics. 7, 141.","mla":"Elul, Yonatan, et al. “Data-Driven Modeling of Interrelated Dynamical Systems.” <i>Communications Physics</i>, vol. 7, 141, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s42005-024-01626-5\">10.1038/s42005-024-01626-5</a>.","ieee":"Y. Elul, E. Rozenberg, A. Boyarski, Y. Yaniv, A. Schuster, and A. M. Bronstein, “Data-driven modeling of interrelated dynamical systems,” <i>Communications Physics</i>, vol. 7. Springer Nature, 2024.","apa":"Elul, Y., Rozenberg, E., Boyarski, A., Yaniv, Y., Schuster, A., &#38; Bronstein, A. M. (2024). Data-driven modeling of interrelated dynamical systems. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-024-01626-5\">https://doi.org/10.1038/s42005-024-01626-5</a>","ama":"Elul Y, Rozenberg E, Boyarski A, Yaniv Y, Schuster A, Bronstein AM. Data-driven modeling of interrelated dynamical systems. <i>Communications Physics</i>. 2024;7. doi:<a href=\"https://doi.org/10.1038/s42005-024-01626-5\">10.1038/s42005-024-01626-5</a>","chicago":"Elul, Yonatan, Eyal Rozenberg, Amit Boyarski, Yael Yaniv, Assaf Schuster, and Alex M. Bronstein. “Data-Driven Modeling of Interrelated Dynamical Systems.” <i>Communications Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s42005-024-01626-5\">https://doi.org/10.1038/s42005-024-01626-5</a>."},"oa":1,"date_updated":"2024-10-09T10:12:11Z","status":"public","type":"journal_article","month":"05","publication_status":"published","author":[{"full_name":"Elul, Yonatan","last_name":"Elul","first_name":"Yonatan"},{"full_name":"Rozenberg, Eyal","last_name":"Rozenberg","first_name":"Eyal"},{"full_name":"Boyarski, Amit","last_name":"Boyarski","first_name":"Amit"},{"last_name":"Yaniv","first_name":"Yael","full_name":"Yaniv, Yael"},{"first_name":"Assaf","last_name":"Schuster","full_name":"Schuster, Assaf"},{"first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander"}],"extern":"1","date_created":"2024-10-08T12:45:35Z","date_published":"2024-05-01T00:00:00Z","publication":"Communications Physics","volume":7,"intvolume":"         7","language":[{"iso":"eng"}],"article_processing_charge":"Yes","abstract":[{"text":"Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems.","lang":"eng"}],"publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s42005-024-01626-5","open_access":"1"}],"quality_controlled":"1","doi":"10.1038/s42005-024-01626-5","publication_identifier":{"issn":["2399-3650"]},"oa_version":"Published Version","article_type":"original","year":"2024"},{"day":"11","issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18205","scopus_import":"1","date_updated":"2024-10-09T10:26:44Z","citation":{"apa":"Wengrowicz, O., Bronstein, A. M., &#38; Cohen, O. (2024). Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. <i>Optics Express</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/oe.515445\">https://doi.org/10.1364/oe.515445</a>","chicago":"Wengrowicz, Omri, Alex M. Bronstein, and Oren Cohen. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” <i>Optics Express</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/oe.515445\">https://doi.org/10.1364/oe.515445</a>.","ama":"Wengrowicz O, Bronstein AM, Cohen O. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. <i>Optics Express</i>. 2024;32(6):8791-8803. doi:<a href=\"https://doi.org/10.1364/oe.515445\">10.1364/oe.515445</a>","short":"O. Wengrowicz, A.M. Bronstein, O. Cohen, Optics Express 32 (2024) 8791–8803.","ista":"Wengrowicz O, Bronstein AM, Cohen O. 2024. Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography. Optics Express. 32(6), 8791–8803.","ieee":"O. Wengrowicz, A. M. Bronstein, and O. Cohen, “Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography,” <i>Optics Express</i>, vol. 32, no. 6. Optica Publishing Group, pp. 8791–8803, 2024.","mla":"Wengrowicz, Omri, et al. “Unsupervised Physics-Informed Deep Learning-Based Reconstruction for Time-Resolved Imaging by Multiplexed Ptychography.” <i>Optics Express</i>, vol. 32, no. 6, Optica Publishing Group, 2024, pp. 8791–803, doi:<a href=\"https://doi.org/10.1364/oe.515445\">10.1364/oe.515445</a>."},"oa":1,"title":"Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography","page":"8791-8803","month":"03","type":"journal_article","status":"public","external_id":{"pmid":["38571128"]},"date_created":"2024-10-08T12:46:01Z","extern":"1","pmid":1,"author":[{"first_name":"Omri","last_name":"Wengrowicz","full_name":"Wengrowicz, Omri"},{"last_name":"Bronstein","orcid":"0000-0001-9699-8730","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander"},{"first_name":"Oren","last_name":"Cohen","full_name":"Cohen, Oren"}],"publication_status":"published","intvolume":"        32","publication":"Optics Express","date_published":"2024-03-11T00:00:00Z","volume":32,"publisher":"Optica Publishing Group","main_file_link":[{"url":"https://doi.org/10.1364/OE.515445","open_access":"1"}],"abstract":[{"lang":"eng","text":"We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms."}],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["1094-4087"]},"quality_controlled":"1","doi":"10.1364/oe.515445","year":"2024","article_type":"original","oa_version":"Published Version"},{"quality_controlled":"1","conference":{"end_date":"2024-09-06","start_date":"2024-09-04","location":"Swansea, United Kingdom","name":"AIiH: Artificial Intelligence in Healthcare"},"doi":"10.1007/978-3-031-67285-9_12","status":"public","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031672859"],"issn":["0302-9743"],"isbn":["9783031672842"]},"alternative_title":["LNCS"],"page":"160-171","month":"08","type":"conference","oa_version":"None","publication_status":"published","author":[{"last_name":"Rave","first_name":"Gilad","full_name":"Rave, Gilad"},{"full_name":"Fordham, Daniel E.","last_name":"Fordham","first_name":"Daniel E."},{"full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","first_name":"Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"full_name":"Silver, David H.","first_name":"David H.","last_name":"Silver"}],"extern":"1","year":"2024","date_created":"2024-10-08T12:46:23Z","scopus_import":"1","_id":"18206","publication":"First International Conference on Artificial Intelligence in Healthcare","date_published":"2024-08-15T00:00:00Z","volume":14976,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     14976","day":"15","title":"Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"mla":"Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” <i>First International Conference on Artificial Intelligence in Healthcare</i>, vol. 14976, Springer Nature, 2024, pp. 160–71, doi:<a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">10.1007/978-3-031-67285-9_12</a>.","ieee":"G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications,” in <i>First International Conference on Artificial Intelligence in Healthcare</i>, Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.","ista":"Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. First International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial Intelligence in Healthcare, LNCS, vol. 14976, 160–171.","short":"G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp. 160–171.","chicago":"Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” In <i>First International Conference on Artificial Intelligence in Healthcare</i>, 14976:160–71. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">https://doi.org/10.1007/978-3-031-67285-9_12</a>.","ama":"Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In: <i>First International Conference on Artificial Intelligence in Healthcare</i>. Vol 14976. Springer Nature; 2024:160-171. doi:<a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">10.1007/978-3-031-67285-9_12</a>","apa":"Rave, G., Fordham, D. E., Bronstein, A. M., &#38; Silver, D. H. (2024). Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In <i>First International Conference on Artificial Intelligence in Healthcare</i> (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-67285-9_12\">https://doi.org/10.1007/978-3-031-67285-9_12</a>"},"abstract":[{"lang":"eng","text":"In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting."}],"publisher":"Springer Nature","date_updated":"2024-10-09T10:33:39Z"},{"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","day":"11","file_date_updated":"2024-10-11T10:04:23Z","_id":"18296","oa":1,"citation":{"apa":"Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>","chicago":"Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>.","ama":"Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>","short":"O. Kim, (2024).","ista":"Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","mla":"Kim, Olena. <i>Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","ieee":"O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024."},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"}],"date_updated":"2026-04-16T12:20:33Z","corr_author":"1","title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","file":[{"content_type":"application/zip","file_size":164382,"success":1,"checksum":"0a977e7df54c418251b10dfd3f8a015c","file_id":"18297","creator":"okim","date_created":"2024-10-11T10:04:19Z","date_updated":"2024-10-11T10:04:19Z","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","relation":"main_file","access_level":"open_access"},{"date_updated":"2024-10-11T10:04:23Z","date_created":"2024-10-11T10:04:23Z","file_name":"info.txt","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_size":654,"success":1,"file_id":"18298","checksum":"5b9343d6b2035ac3185e390fad4d3830","creator":"okim"}],"month":"10","type":"research_data","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Hippocampal mossy fiber synapses","short-term potentiation","long-term potentiation","presynaptic plasticity","electron microscopy","freeze-fracture replica labeling","paired recordings","forskolin","cyclic adenosine monophosphate (cAMP)","protein kinase A (PKA)","neuromodulation","synaptic vesicle pools","presynaptic Ca2+ channels","Munc13","docking","priming","active zone"],"department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"date_created":"2024-10-11T10:12:17Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18603"}]},"author":[{"first_name":"Olena","orcid":"0000-0003-2344-1039","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena"}],"date_published":"2024-10-11T00:00:00Z","ec_funded":1,"abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","contributor":[{"first_name":"Olena","last_name":"Kim","contributor_type":"researcher","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Okamoto","orcid":"0000-0003-0408-6094","first_name":"Yuji","contributor_type":"researcher","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","contributor_type":"researcher","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","first_name":"Nils ","last_name":"Brose"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","contributor_type":"supervisor","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","doi":"10.15479/AT:ISTA:18296","has_accepted_license":"1","year":"2024","ddc":["570"],"oa_version":"Submitted Version"}]