[{"oa_version":"Published Version","language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-16","start_date":"2023-12-10","name":"NeurIPS: Neural Information Processing Systems","location":"New Orleans, LA, United States"},"external_id":{"arxiv":["2310.16752"]},"volume":36,"year":"2023","project":[{"call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer"}],"abstract":[{"text":"Clustering is a fundamental problem in unsupervised machine learning with many applications in data analysis. Popular clustering algorithms such as Lloyd's algorithm and k-means++ can make Ω(ndk) time when clustering n points in a d-dimensional space (represented by an n×d matrix X) into k clusters. On massive datasets with moderate to large k, the multiplicative \r\nk factor can become very expensive. We introduce a simple randomized clustering algorithm that provably runs in expected time O(nnz(X)+nlogn) for arbitrary k. Here nnz(X) is the total number of non-zero entries in the input dataset X, which is upper bounded by nd and can be significantly smaller for sparse datasets. We prove that our algorithm achieves approximation ratio ˜O(k4) on any input dataset for the k-means objective, and our experiments show that the quality of the clusters found by our algorithm is usually much better than this worst-case bound. We use our algorithm for k-means clustering and for coreset construction; our experiments show that it gives a new tradeoff between running time and cluster quality compared to previous state-of-the-art methods for these tasks. Our theoretical analysis is based on novel results of independent interest. We show that the approximation ratio achieved after a random one-dimensional projection can be lifted to the original points and that k-means++ seeding can be implemented in expected time O(nlogn) in one dimension.","lang":"eng"}],"file":[{"file_size":1445159,"success":1,"file_name":"2023_Neurips_Charikar.pdf","date_updated":"2024-05-22T07:34:00Z","date_created":"2024-05-22T07:34:00Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"d169a147a2adf55878e0a99e36a9d468","file_id":"15416","content_type":"application/pdf"}],"_id":"15364","date_updated":"2026-07-07T06:37:54Z","status":"public","article_processing_charge":"Yes","department":[{"_id":"MoHe"}],"intvolume":"        36","has_accepted_license":"1","publisher":"Neural Information Processing Systems Foundation","alternative_title":["Advances in Neural Information Processing Systems"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Moses Charikar was supported by a Simons Investigator award. Lunjia Hu was supported by Moses Charikar’s and Omer Reingold’s Simons Investigators awards, Omer Reingold’s NSF Award IIS-1908774, and the Simons Foundation Collaboration on the Theory of Algorithmic Fairness. Part of this work was done while Erik Waingarten was a postdoc at Stanford University, supported by an NSF postdoctoral fellowship and by Moses Charikar’s Simons\r\nInvestigator Award. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme\r\n(Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data\r\nStructures (MoDynStruct)” and the Austrian Science Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","ddc":["000"],"oa":1,"das_tickbox":"1","day":"15","scopus_import":"1","date_published":"2023-12-15T00:00:00Z","file_date_updated":"2024-05-22T07:34:00Z","publication_status":"published","month":"12","author":[{"full_name":"Charikar, Moses","last_name":"Charikar","first_name":"Moses"},{"full_name":"Hu, Lunjia","last_name":"Hu","first_name":"Lunjia"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"last_name":"Vötsch","first_name":"Maximilian","full_name":"Vötsch, Maximilian"},{"full_name":"Waingarten, Erik","first_name":"Erik","last_name":"Waingarten"}],"date_created":"2024-05-05T22:01:05Z","type":"conference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"ec_funded":1,"title":"Simple, scalable and effective clustering via one-dimensional projections","publication":"37th Conference on Neural Information Processing Systems","arxiv":1,"publication_identifier":{"issn":["1049-5258"]},"citation":{"ieee":"M. Charikar, L. Hu, M. Henzinger, M. Vötsch, and E. Waingarten, “Simple, scalable and effective clustering via one-dimensional projections,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023, vol. 36.","ista":"Charikar M, Hu L, Henzinger M, Vötsch M, Waingarten E. 2023. Simple, scalable and effective clustering via one-dimensional projections. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36.","apa":"Charikar, M., Hu, L., Henzinger, M., Vötsch, M., &#38; Waingarten, E. (2023). Simple, scalable and effective clustering via one-dimensional projections. In <i>37th Conference on Neural Information Processing Systems</i> (Vol. 36). New Orleans, LA, United States: Neural Information Processing Systems Foundation.","ama":"Charikar M, Hu L, Henzinger M, Vötsch M, Waingarten E. Simple, scalable and effective clustering via one-dimensional projections. In: <i>37th Conference on Neural Information Processing Systems</i>. Vol 36. Neural Information Processing Systems Foundation; 2023.","mla":"Charikar, Moses, et al. “Simple, Scalable and Effective Clustering via One-Dimensional Projections.” <i>37th Conference on Neural Information Processing Systems</i>, vol. 36, Neural Information Processing Systems Foundation, 2023.","short":"M. Charikar, L. Hu, M. Henzinger, M. Vötsch, E. Waingarten, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023.","chicago":"Charikar, Moses, Lunjia Hu, Monika Henzinger, Maximilian Vötsch, and Erik Waingarten. “Simple, Scalable and Effective Clustering via One-Dimensional Projections.” In <i>37th Conference on Neural Information Processing Systems</i>, Vol. 36. Neural Information Processing Systems Foundation, 2023."},"quality_controlled":"1"},{"file":[{"file_name":"2023_Neurips_Safaryan.pdf","file_size":672571,"success":1,"date_updated":"2024-05-22T08:08:08Z","date_created":"2024-05-22T08:08:08Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"288c5148a85abf24ad5e22a6b1183655","file_id":"15417","content_type":"application/pdf"}],"corr_author":"1","abstract":[{"text":"Knowledge distillation is a popular approach for enhancing the performance of \"student\" models, with lower representational capacity, by taking advantage of more powerful \"teacher\" models. Despite its apparent simplicity, the underlying mechanics behind knowledge distillation (KD) are not yet fully understood. In this work, we shed new light on the inner workings of this method, by examining it from an optimization perspective. Specifically, we show that, in the context of linear and deep linear models, KD can be interpreted as a novel type of stochastic variance reduction mechanism. We provide a detailed convergence analysis of the resulting dynamics, which hold under standard assumptions for both strongly-convex and non-convex losses, showing that KD acts as a form of \\emph{partial variance reduction}, which can reduce the stochastic gradient noise, but may not eliminate it completely, depending on the properties of the teacher'' model. Our analysis puts further emphasis on the need for careful parametrization of KD, in particular w.r.t. the weighting of the distillation loss, and is validated empirically on both linear models and deep neural networks.","lang":"eng"}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"year":"2023","volume":36,"conference":{"start_date":"2023-12-10","end_date":"2023-12-16","location":"New Orleans, LA, United States","name":"NeurIPS: Neural Information Processing Systems"},"external_id":{"arxiv":["2305.17581"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"        36","department":[{"_id":"DaAl"}],"article_processing_charge":"Yes","date_updated":"2026-07-07T06:37:28Z","status":"public","_id":"15363","alternative_title":["Advances in Neural Information Processing Systems"],"has_accepted_license":"1","publisher":"Neural Information Processing Systems Foundation","oa":1,"ddc":["000"],"acknowledgement":"MS has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No 101034413.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-12-15T00:00:00Z","file_date_updated":"2024-05-22T08:08:08Z","publication_status":"published","scopus_import":"1","day":"15","das_tickbox":"1","ec_funded":1,"type":"conference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_created":"2024-05-05T22:01:04Z","author":[{"first_name":"Mher","last_name":"Safaryan","id":"dd546b39-0804-11ed-9c55-ef075c39778d","full_name":"Safaryan, Mher"},{"last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"}],"month":"12","citation":{"short":"M. Safaryan, A. Krumes, D.-A. Alistarh, in:, 36th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023.","chicago":"Safaryan, Mher, Alexandra Krumes, and Dan-Adrian Alistarh. “Knowledge Distillation Performs Partial Variance Reduction.” In <i>36th Conference on Neural Information Processing Systems</i>, Vol. 36. Neural Information Processing Systems Foundation, 2023.","ieee":"M. Safaryan, A. Krumes, and D.-A. Alistarh, “Knowledge distillation performs partial variance reduction,” in <i>36th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023, vol. 36.","mla":"Safaryan, Mher, et al. “Knowledge Distillation Performs Partial Variance Reduction.” <i>36th Conference on Neural Information Processing Systems</i>, vol. 36, Neural Information Processing Systems Foundation, 2023.","ama":"Safaryan M, Krumes A, Alistarh D-A. Knowledge distillation performs partial variance reduction. In: <i>36th Conference on Neural Information Processing Systems</i>. Vol 36. Neural Information Processing Systems Foundation; 2023.","apa":"Safaryan, M., Krumes, A., &#38; Alistarh, D.-A. (2023). Knowledge distillation performs partial variance reduction. In <i>36th Conference on Neural Information Processing Systems</i> (Vol. 36). New Orleans, LA, United States: Neural Information Processing Systems Foundation.","ista":"Safaryan M, Krumes A, Alistarh D-A. 2023. Knowledge distillation performs partial variance reduction. 36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36."},"publication_identifier":{"issn":["1049-5258"]},"arxiv":1,"publication":"36th Conference on Neural Information Processing Systems","title":"Knowledge distillation performs partial variance reduction","quality_controlled":"1"},{"das_tickbox":"1","day":"15","date_published":"2023-12-15T00:00:00Z","publication_status":"published","month":"12","author":[{"full_name":"Súkeník, Peter","last_name":"Súkeník","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","first_name":"Peter"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"date_created":"2024-02-02T11:17:41Z","type":"conference","title":"Deep neural collapse is provably optimal for the deep unconstrained features model","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2305.13165","open_access":"1"}],"publication":"37th Conference on Neural Information Processing Systems","arxiv":1,"citation":{"ieee":"P. Súkeník, M. Mondelli, and C. Lampert, “Deep neural collapse is provably optimal for the deep unconstrained features model,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023.","apa":"Súkeník, P., Mondelli, M., &#38; Lampert, C. (2023). Deep neural collapse is provably optimal for the deep unconstrained features model. In <i>37th Conference on Neural Information Processing Systems</i>. New Orleans, LA, United States: Neural Information Processing Systems Foundation.","ama":"Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. In: <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation; 2023.","ista":"Súkeník P, Mondelli M, Lampert C. 2023. Deep neural collapse is provably optimal for the deep unconstrained features model. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, .","mla":"Súkeník, Peter, et al. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” <i>37th Conference on Neural Information Processing Systems</i>, Neural Information Processing Systems Foundation, 2023.","short":"P. Súkeník, M. Mondelli, C. Lampert, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023.","chicago":"Súkeník, Peter, Marco Mondelli, and Christoph Lampert. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” In <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation, 2023."},"publication_identifier":{"eissn":["1049-5258"]},"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"arxiv":["2305.13165"]},"conference":{"start_date":"2023-12-10","end_date":"2023-12-16","location":"New Orleans, LA, United States","name":"NeurIPS: Neural Information Processing Systems"},"year":"2023","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"abstract":[{"text":"Neural collapse (NC) refers to the surprising structure of the last layer of deep neural networks in the terminal phase of gradient descent training. Recently, an increasing amount of experimental evidence has pointed to the propagation of NC to earlier layers of neural networks. However, while the NC in the last layer is well studied theoretically, much less is known about its multi-layered counterpart - deep neural collapse (DNC). In particular, existing work focuses either on linear layers or only on the last two layers at the price of an extra assumption. Our paper fills this gap by generalizing the established analytical framework for NC - the unconstrained features model - to multiple non-linear layers. Our key technical contribution is to show that, in a deep unconstrained features model, the unique global optimum for binary classification exhibits all the properties typical of DNC. This explains the existing experimental evidence of DNC. We also empirically show that (i) by optimizing deep unconstrained features models via gradient descent, the resulting solution agrees well with our theory, and (ii) trained networks recover the unconstrained features suitable for the occurrence of DNC, thus supporting the validity of this modeling principle.","lang":"eng"}],"corr_author":"1","_id":"14921","date_updated":"2026-07-07T06:35:57Z","status":"public","article_processing_charge":"No","department":[{"_id":"MaMo"},{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems Foundation","alternative_title":["Advances in Neural Information Processing Systems"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"M. M. is partially supported by the 2019 Lopez-Loreta Prize. The authors would like to thank Eugenia Iofinova, Bernd Prach and Simone Bombari for valuable feedback on the manuscript.","oa":1},{"has_accepted_license":"1","publisher":"Springer Nature","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"oa":1,"isi":1,"file":[{"creator":"dernst","date_created":"2023-09-06T08:16:25Z","date_updated":"2023-09-06T08:16:25Z","file_size":421408,"file_name":"2023_LNCS_Koval.pdf","success":1,"content_type":"application/pdf","file_id":"14275","checksum":"c346016393123a0a2338ad4d976f61bc","access_level":"open_access","relation":"main_file"}],"abstract":[{"lang":"eng","text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness."}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2023","volume":13964,"conference":{"end_date":"2023-07-22","start_date":"2023-07-17","name":"CAV: Computer Aided Verification","location":"Paris, France"},"external_id":{"isi":["001310786500008"]},"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"intvolume":"     13964","page":"156-169","_id":"14260","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-07-07T13:39:36Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14995"}]},"status":"public","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031377051"],"eissn":["1611-3349"]},"citation":{"mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification</i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification</i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification</i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13964, pp. 156–169.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification</i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 156–169."},"doi":"10.1007/978-3-031-37706-8_8","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","publication":"35th International Conference on Computer Aided Verification","quality_controlled":"1","day":"17","fulldoi":"https://doi.org/10.1007/978-3-031-37706-8_8","publication_status":"published","date_published":"2023-07-17T00:00:00Z","file_date_updated":"2023-09-06T08:16:25Z","scopus_import":"1","das_tickbox":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"conference","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"full_name":"Sokolova, Maria","first_name":"Maria","last_name":"Sokolova"},{"first_name":"Dmitry","last_name":"Tsitelov","full_name":"Tsitelov, Dmitry"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"month":"07","date_created":"2023-09-03T22:01:16Z"},{"citation":{"ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in <i>35th International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13964, pp. 390–414.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: <i>35th International Conference on Computer Aided Verification</i>. Vol 13964. Springer Nature; 2023:390-414. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., &#38; Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In <i>35th International Conference on Computer Aided Verification</i> (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” <i>35th International Conference on Computer Aided Verification</i>, vol. 13964, Springer Nature, 2023, pp. 390–414, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 390–414.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In <i>35th International Conference on Computer Aided Verification</i>, 13964:390–414. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>."},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"doi":"10.1007/978-3-031-37706-8_20","title":"Guessing winning policies in LTL synthesis by semantic learning","publication":"35th International Conference on Computer Aided Verification","quality_controlled":"1","fulldoi":"https://doi.org/10.1007/978-3-031-37706-8_20","day":"17","scopus_import":"1","date_published":"2023-07-17T00:00:00Z","publication_status":"published","file_date_updated":"2023-09-06T08:25:50Z","das_tickbox":"1","type":"conference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"month":"07","author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan"},{"first_name":"Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"full_name":"Prokop, Maximilian","last_name":"Prokop","first_name":"Maximilian"},{"first_name":"Sabine","last_name":"Rieder","full_name":"Rieder, Sabine"}],"date_created":"2023-09-03T22:01:16Z","has_accepted_license":"1","publisher":"Springer Nature","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","oa":1,"ddc":["000"],"isi":1,"abstract":[{"text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.","lang":"eng"}],"file":[{"file_name":"2023_LNCS_CAV_Kretinsky.pdf","file_size":428354,"success":1,"creator":"dernst","date_created":"2023-09-06T08:25:50Z","date_updated":"2023-09-06T08:25:50Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14276","checksum":"ed66278b61bb869e1baba3d9b9081271"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["001310786500020"]},"conference":{"name":"CAV: Computer Aided Verification","location":"Paris, France","end_date":"2023-07-22","start_date":"2023-07-17"},"volume":13964,"year":"2023","department":[{"_id":"KrCh"}],"intvolume":"     13964","_id":"14259","page":"390-414","date_updated":"2026-07-07T13:39:23Z","status":"public","article_processing_charge":"Yes (in subscription journal)"},{"oa":1,"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5281/ZENODO.7877757","citation":{"chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7877757\">https://doi.org/10.5281/ZENODO.7877757</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023).","mla":"Koval, Nikita, et al. <i>Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7877757\">https://doi.org/10.5281/ZENODO.7877757</a>","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM.” Zenodo, 2023."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7877757"}],"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","publisher":"Zenodo","department":[{"_id":"DaAl"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","id":"14260","relation":"used_in_publication"}]},"status":"public","date_created":"2024-02-14T15:14:13Z","date_updated":"2026-07-07T13:39:35Z","article_processing_charge":"No","_id":"14995","month":"04","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"last_name":"Sokolova","first_name":"Maria","full_name":"Sokolova, Maria"},{"last_name":"Tsitelov","first_name":"Dmitry","full_name":"Tsitelov, Dmitry"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"abstract":[{"text":"Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. \r\nThe artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation.","lang":"eng"}],"date_published":"2023-04-28T00:00:00Z","fulldoi":"https://doi.org/10.5281/ZENODO.7877757","day":"28","year":"2023","oa_version":"Published Version"},{"date_created":"2023-05-14T22:01:00Z","author":[{"last_name":"Boissonnat","first_name":"Jean Daniel","full_name":"Boissonnat, Jean Daniel"},{"full_name":"Kachanovich, Siargey","last_name":"Kachanovich","first_name":"Siargey"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken"}],"month":"04","ec_funded":1,"type":"journal_article","date_published":"2023-04-30T00:00:00Z","article_type":"original","publication_status":"published","scopus_import":"1","day":"30","fulldoi":"https://doi.org/10.1137/21M1412918","quality_controlled":"1","issue":"2","publication":"SIAM Journal on Computing","main_file_link":[{"open_access":"1","url":"https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1"}],"title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations","doi":"10.1137/21M1412918","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"citation":{"short":"J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing 52 (2023) 452–486.","chicago":"Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/21M1412918\">https://doi.org/10.1137/21M1412918</a>.","ieee":"J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,” <i>SIAM Journal on Computing</i>, vol. 52, no. 2. Society for Industrial and Applied Mathematics, pp. 452–486, 2023.","mla":"Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” <i>SIAM Journal on Computing</i>, vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86, doi:<a href=\"https://doi.org/10.1137/21M1412918\">10.1137/21M1412918</a>.","apa":"Boissonnat, J. D., Kachanovich, S., &#38; Wintraecken, M. (2023). Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1412918\">https://doi.org/10.1137/21M1412918</a>","ama":"Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. <i>SIAM Journal on Computing</i>. 2023;52(2):452-486. doi:<a href=\"https://doi.org/10.1137/21M1412918\">10.1137/21M1412918</a>","ista":"Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 52(2), 452–486."},"article_processing_charge":"No","status":"public","date_updated":"2026-07-07T13:43:40Z","related_material":{"record":[{"id":"9441","relation":"earlier_version","status":"public"}]},"page":"452-486","_id":"12960","intvolume":"        52","department":[{"_id":"HeEd"}],"year":"2023","volume":52,"external_id":{"isi":["001013183000012"]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","corr_author":"1","abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M^ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. "}],"isi":1,"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"oa":1,"acknowledgement":"The authors have received funding from the European Research Council under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations of Geometric Un-derstanding  in  Higher  Dimensions).   The  first  author  was  supported  by  the  French  government,through the 3IA C\\^ote d'Azur Investments in the Future project managed by the National ResearchAgency (ANR) with the reference ANR-19-P3IA-0002.  The third author was supported by the Eu-ropean Union's Horizon 2020 research and innovation programme under the Marie Sk\\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science Fund) grant M 3073.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics"},{"has_accepted_license":"1","publisher":"EDP Sciences","oa":1,"ddc":["520"],"acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","volume":676,"external_id":{"arxiv":["2306.11587"],"isi":["001046037700007"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","file":[{"file_size":458120,"file_name":"2023_AstronomyAstrophysics_Mathis.pdf","success":1,"creator":"dernst","date_created":"2023-09-06T07:13:19Z","date_updated":"2023-09-06T07:13:19Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14271","checksum":"7b30d26fb2b7bcb5b5be1414950615f9"}],"abstract":[{"lang":"eng","text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries."}],"isi":1,"article_processing_charge":"Yes (in subscription journal)","status":"public","date_updated":"2026-07-08T06:45:55Z","_id":"14256","intvolume":"       676","department":[{"_id":"LiBu"}],"publication":"Astronomy & Astrophysics","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","doi":"10.1051/0004-6361/202346832","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"citation":{"chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>.","short":"S. Mathis, L.A. Bugnet, Astronomy &#38; Astrophysics 676 (2023).","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy &#38; Astrophysics. 676, L9.","apa":"Mathis, S., &#38; Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy &#38; Astrophysics</i>. 2023;676. doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy &#38; Astrophysics</i>, vol. 676, L9, EDP Sciences, 2023, doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>.","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” <i>Astronomy &#38; Astrophysics</i>, vol. 676. EDP Sciences, 2023."},"arxiv":1,"quality_controlled":"1","das_tickbox":"1","publication_status":"published","date_published":"2023-08-01T00:00:00Z","file_date_updated":"2023-09-06T07:13:19Z","article_type":"letter_note","scopus_import":"1","day":"01","fulldoi":"https://doi.org/10.1051/0004-6361/202346832","date_created":"2023-09-03T22:01:15Z","author":[{"full_name":"Mathis, S.","first_name":"S.","last_name":"Mathis"},{"full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle"}],"month":"08","article_number":"L9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article"},{"title":"Resonant microwave spectroscopy of Al-InAs","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>","mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>."},"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/14547","author":[{"first_name":"Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T"}],"month":"11","degree_awarded":"PhD","date_created":"2023-11-17T13:45:26Z","type":"dissertation","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"OA_place":"publisher","day":"16","fulldoi":"https://doi.org/10.15479/14547","file_date_updated":"2023-11-22T09:46:06Z","publication_status":"published","date_published":"2023-11-16T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["530"],"oa":1,"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363"}],"alternative_title":["ISTA Thesis"],"page":"80","_id":"14547","article_processing_charge":"No","status":"public","related_material":{"record":[{"status":"public","id":"10851","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13264","status":"public"}]},"date_updated":"2026-07-08T08:38:43Z","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2023","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"file":[{"file_id":"14548","content_type":"application/pdf","checksum":"db0c37d213bc002125bd59690e9db246","access_level":"open_access","relation":"main_file","creator":"pduc","date_updated":"2023-11-22T09:46:06Z","date_created":"2023-11-17T13:36:44Z","file_size":34828019,"file_name":"Phan_Thesis_pdfa.pdf"},{"date_updated":"2023-11-17T13:47:54Z","date_created":"2023-11-17T13:44:53Z","creator":"pduc","file_size":279319709,"file_name":"dissertation_src.zip","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","content_type":"application/zip","file_id":"14549","relation":"source_file","access_level":"closed"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}]},{"issue":"15","quality_controlled":"1","publication_identifier":{"eissn":["1539-4794"],"issn":["0146-9592"]},"citation":{"chicago":"Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofia Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” <i>Optics Letters</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ol.495553\">https://doi.org/10.1364/ol.495553</a>.","short":"U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976.","apa":"Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., &#38; Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ol.495553\">https://doi.org/10.1364/ol.495553</a>","ama":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. <i>Optics Letters</i>. 2023;48(15):3973-3976. doi:<a href=\"https://doi.org/10.1364/ol.495553\">10.1364/ol.495553</a>","ista":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976.","mla":"Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” <i>Optics Letters</i>, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:<a href=\"https://doi.org/10.1364/ol.495553\">10.1364/ol.495553</a>.","ieee":"U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” <i>Optics Letters</i>, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023."},"arxiv":1,"doi":"10.1364/ol.495553","title":"Monitoring and active stabilization of laser injection locking using beam ellipticity","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01266"}],"publication":"Optics Letters","type":"journal_article","author":[{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","last_name":"Mishra","first_name":"Umang","full_name":"Mishra, Umang"},{"last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","first_name":"Vyacheslav","full_name":"Li, Vyacheslav"},{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","last_name":"Wald","orcid":"0000-0002-5869-1604","first_name":"Sebastian","full_name":"Wald, Sebastian"},{"full_name":"Agafonova, Sofya","first_name":"Sofya","orcid":"0000-0003-0582-2946","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","last_name":"Agafonova"},{"orcid":"0000-0002-4947-8924","first_name":"Fritz R","last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","full_name":"Diorico, Fritz R"},{"first_name":"Onur","orcid":"0000-0002-2031-204X","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur"}],"month":"07","date_created":"2024-01-08T13:01:46Z","day":"21","fulldoi":"https://doi.org/10.1364/ol.495553","date_published":"2023-07-21T00:00:00Z","publication_status":"published","article_type":"original","scopus_import":"1","das_tickbox":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","oa":1,"supplementarymaterial":"no","publisher":"Optica Publishing Group","department":[{"_id":"OnHo"}],"intvolume":"        48","page":"3973-3976","_id":"14749","article_processing_charge":"No","date_updated":"2026-07-08T08:41:47Z","status":"public","isi":1,"abstract":[{"text":"We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry.","lang":"eng"}],"corr_author":"1","dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","language":[{"iso":"eng"}],"oa_version":"Preprint","volume":48,"researchdata_availability":"upon request","year":"2023","keyword":["Atomic and Molecular Physics","and Optics"],"external_id":{"arxiv":["2212.01266"],"isi":["001051044600008"]}},{"abstract":[{"lang":"eng","text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters."}],"corr_author":"1","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"isi":1,"volume":107,"year":"2023","researchdata_availability":"no","external_id":{"isi":["001019748000005"],"arxiv":["2302.01022"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"       107","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"article_processing_charge":"No","status":"public","date_updated":"2026-07-08T08:30:05Z","_id":"13233","supplementarymaterial":"yes","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_type":"letter_note","publication_status":"published","date_published":"2023-06-20T00:00:00Z","scopus_import":"1","day":"20","fulldoi":"https://doi.org/10.1103/PhysRevA.107.L061304","das_tickbox":"0","ec_funded":1,"type":"journal_article","date_created":"2023-07-16T22:01:10Z","author":[{"full_name":"Agafonova, Sofya","first_name":"Sofya","orcid":"0000-0003-0582-2946","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","last_name":"Agafonova"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"article_number":"L061304","month":"06","doi":"10.1103/PhysRevA.107.L061304","citation":{"chicago":"Agafonova, Sofia, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","apa":"Agafonova, S., Lemeshko, M., &#38; Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>","mla":"Agafonova, Sofia, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>.","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023."},"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"arxiv":1,"publication":"Physical Review A","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.01022"}],"title":"Finite-range bias in fitting three-body loss to the zero-range model","quality_controlled":"1","issue":"6"},{"publisher":"American Physical Society","supplementarymaterial":"yes","oa":1,"acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"dataavailabilitystatement":"The raw data and the plotting code are available in the Supplemental Material at http://link.aps.org/supplemental/10.1103/PhysRevApplied.19.064032. Further data are available upon reasonable request.","corr_author":"1","isi":1,"researchdata_availability":"yes (supplementary data)","volume":19,"year":"2023","external_id":{"isi":["001012022600004"],"arxiv":["2206.05746"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"        19","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"article_processing_charge":"No","date_updated":"2026-07-08T08:38:44Z","related_material":{"record":[{"id":"14547","relation":"dissertation_contains","status":"public"}]},"status":"public","_id":"13264","doi":"10.1103/PhysRevApplied.19.064032","publication_identifier":{"eissn":["2331-7019"]},"citation":{"ieee":"D. T. Phan <i>et al.</i>, “Gate-tunable superconductor-semiconductor parametric amplifier,” <i>Physical Review Applied</i>, vol. 19, no. 6. American Physical Society, 2023.","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., &#38; Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>."},"arxiv":1,"publication":"Physical Review Applied","title":"Gate-tunable superconductor-semiconductor parametric amplifier","main_file_link":[{"url":"https://arxiv.org/abs/2206.05746","open_access":"1"}],"quality_controlled":"1","issue":"6","article_type":"original","date_published":"2023-06-09T00:00:00Z","publication_status":"published","scopus_import":"1","day":"09","fulldoi":"https://doi.org/10.1103/PhysRevApplied.19.064032","das_tickbox":"1","type":"journal_article","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_created":"2023-07-23T22:01:12Z","author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan","first_name":"Duc T","full_name":"Phan, Duc T"},{"first_name":"Paul","last_name":"Falthansl-Scheinecker","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","full_name":"Falthansl-Scheinecker, Paul"},{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","last_name":"Mishra","first_name":"Umang","full_name":"Mishra, Umang"},{"last_name":"Strickland","first_name":"W. M.","full_name":"Strickland, W. M."},{"full_name":"Langone, D.","first_name":"D.","last_name":"Langone"},{"full_name":"Shabani, J.","first_name":"J.","last_name":"Shabani"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P"}],"month":"06","article_number":"064032"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn"}],"page":"104","_id":"14641","article_processing_charge":"No","date_updated":"2026-07-13T10:55:56Z","status":"public","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2023","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"access_level":"closed","relation":"source_file","file_id":"14648","content_type":"application/vnd.oasis.opendocument.text","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_name":"mike_thesis_v06-12-2023.odt","file_size":46405919,"embargo_to":"open_access","creator":"mhenness","date_updated":"2024-11-30T23:30:05Z","date_created":"2023-12-06T13:13:26Z"},{"date_updated":"2026-07-13T10:55:56Z","date_created":"2023-12-06T13:14:15Z","creator":"mhenness","embargo_to":"open_access","file_name":"mike_thesis_v06-12-2023.pdf","embargo":"2026-11-18","file_size":21282155,"checksum":"f5203a61eddaf35235bbc51904d73982","file_id":"14649","content_type":"application/pdf","relation":"main_file","access_level":"closed"},{"checksum":"902102d26d30e74dbd6cdd70a65820c3","title":"Print version","file_id":"19720","content_type":"application/pdf","relation":"other","description":"for printing purposes only","access_level":"closed","date_created":"2025-05-20T12:59:12Z","date_updated":"2025-05-20T22:31:34Z","creator":"cchlebak","embargo_to":"open_access","file_name":"2023_Hennessey_Michael_Thesis_print.pdf","file_size":45847968}],"abstract":[{"text":"Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments.","lang":"eng"}],"corr_author":"1","title":"Adaptive mutation in E. coli modulated by luxS","publication_identifier":{"issn":["2663-337X"]},"citation":{"chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023."},"doi":"10.15479/at:ista:14641","author":[{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","last_name":"Hennessey-Wesen","first_name":"Mike","full_name":"Hennessey-Wesen, Mike"}],"month":"11","date_created":"2023-12-04T13:17:37Z","degree_awarded":"PhD","type":"dissertation","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"ec_funded":1,"das_tickbox":"1","OA_place":"publisher","day":"30","fulldoi":"https://doi.org/10.15479/at:ista:14641","publication_status":"published","file_date_updated":"2026-07-13T10:55:56Z","date_published":"2023-11-30T00:00:00Z"},{"article_type":"original","file_date_updated":"2023-12-11T12:45:12Z","publication_status":"published","date_published":"2023-11-21T00:00:00Z","scopus_import":"1","OA_type":"hybrid","day":"21","fulldoi":"https://doi.org/10.1073/pnas.2306525120","OA_place":"publisher","das_tickbox":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","date_created":"2023-12-10T23:01:00Z","author":[{"id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","last_name":"Chintaluri","first_name":"Chaitanya","orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"}],"article_number":"e2306525120","month":"11","doi":"10.1073/pnas.2306525120","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 48. National Academy of Sciences, 2023.","apa":"Chintaluri, C., &#38; Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2306525120\">https://doi.org/10.1073/pnas.2306525120</a>","ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(48). doi:<a href=\"https://doi.org/10.1073/pnas.2306525120\">10.1073/pnas.2306525120</a>","ista":"Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120.","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2306525120\">10.1073/pnas.2306525120</a>.","short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2306525120\">https://doi.org/10.1073/pnas.2306525120</a>."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","pmid":1,"quality_controlled":"1","issue":"48","file":[{"date_created":"2023-12-11T12:45:12Z","date_updated":"2023-12-11T12:45:12Z","creator":"dernst","success":1,"file_size":16891602,"file_name":"2023_PNAS_Chintaluri.pdf","checksum":"bf4ec38602a70dae4338077a5a4d497f","file_id":"14678","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"abstract":[{"text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function.","lang":"eng"}],"corr_author":"1","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"isi":1,"year":"2023","volume":120,"external_id":{"pmid":["37988463"],"isi":["001157389000005"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":"       120","department":[{"_id":"TiVo"}],"article_processing_charge":"Yes (in subscription journal)","related_material":{"link":[{"relation":"software","url":"https://github.com/ccluri/metabolic_spiking"}]},"status":"public","date_updated":"2026-07-13T12:30:49Z","_id":"14666","has_accepted_license":"1","publisher":"National Academy of Sciences","ddc":["570"],"oa":1,"acknowledgement":"We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"        62","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"article_processing_charge":"Yes (via OA deal)","date_updated":"2026-07-20T09:49:12Z","status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"12497"},{"status":"public","relation":"other","id":"14861"},{"status":"public","relation":"dissertation_contains","id":"22334"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/","description":"News on ISTA website"}]},"_id":"12675","file":[{"date_updated":"2023-08-16T12:33:31Z","date_created":"2023-08-16T12:33:31Z","creator":"dernst","success":1,"file_size":1422445,"file_name":"2023_AngewChemInt_Becker.pdf","checksum":"7dd083ed8850faa55c34e411ed390de9","file_id":"14072","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"corr_author":"1","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"isi":1,"volume":62,"year":"2023","keyword":["General Chemistry","Catalysis"],"external_id":{"isi":["000956919900001"],"pmid":["36738230"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["540"],"oa":1,"acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Wiley","type":"journal_article","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_created":"2023-02-24T10:45:01Z","author":[{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","full_name":"Becker, Lea Marie"},{"full_name":"Berbon, Mélanie","last_name":"Berbon","first_name":"Mélanie"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"full_name":"Grelard, Axelle","first_name":"Axelle","last_name":"Grelard"},{"full_name":"Morvan, Estelle","first_name":"Estelle","last_name":"Morvan"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"},{"full_name":"Loquet, Antoine","last_name":"Loquet","first_name":"Antoine"},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"month":"05","article_number":"e202219314","publication_status":"published","article_type":"original","date_published":"2023-05-01T00:00:00Z","file_date_updated":"2023-08-16T12:33:31Z","scopus_import":"1","day":"01","fulldoi":"https://doi.org/10.1002/anie.202219314","pmid":1,"quality_controlled":"1","issue":"19","doi":"10.1002/anie.202219314","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"citation":{"ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. 2023;62(19). doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>","mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>.","ieee":"L. M. Becker <i>et al.</i>, “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19. Wiley, 2023.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023)."},"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Angewandte Chemie International Edition","title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues"},{"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Journal of Structural Biology: X","citation":{"ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. 2023;7. doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., &#38; Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>, vol. 7, 100079, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” <i>Journal of Structural Biology: X</i>, vol. 7. Elsevier, 2023.","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023)."},"publication_identifier":{"issn":["2590-1524"]},"doi":"10.1016/j.yjsbx.2022.100079","pmid":1,"quality_controlled":"1","day":"01","fulldoi":"https://doi.org/10.1016/j.yjsbx.2022.100079","publication_status":"published","article_type":"original","file_date_updated":"2023-08-16T09:36:28Z","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","author":[{"full_name":"Gauto, Diego F.","first_name":"Diego F.","last_name":"Gauto"},{"full_name":"Lebedenko, Olga O.","first_name":"Olga O.","last_name":"Lebedenko"},{"last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","full_name":"Becker, Lea Marie"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"first_name":"Nikolai R.","last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R."},{"full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_number":"100079","month":"01","date_created":"2023-01-12T11:55:38Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publisher":"Elsevier","has_accepted_license":"1","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["570"],"language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2023","volume":7,"keyword":["Structural Biology"],"external_id":{"pmid":["36578472"]},"file":[{"access_level":"open_access","relation":"main_file","file_id":"14064","content_type":"application/pdf","checksum":"b4b1c10a31018aafe053b7d55a470e54","file_size":5132322,"file_name":"2023_JourStrucBiologyX_Gauto.pdf","success":1,"creator":"dernst","date_created":"2023-08-16T09:36:28Z","date_updated":"2023-08-16T09:36:28Z"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects."}],"_id":"12114","article_processing_charge":"No","date_updated":"2026-07-20T09:49:12Z","status":"public","related_material":{"record":[{"status":"public","id":"22334","relation":"dissertation_contains"}]},"department":[{"_id":"PaSc"}],"intvolume":"         7"},{"department":[{"_id":"MaIb"}],"intvolume":"        11","_id":"13968","article_processing_charge":"Yes","related_material":{"record":[{"id":"19308","relation":"research_data","status":"public"}]},"date_updated":"2026-07-22T06:16:47Z","status":"public","isi":1,"file":[{"file_size":2421758,"success":1,"file_name":"2023_FrontiersPhysics_Hasler.pdf","date_created":"2023-08-07T07:48:11Z","date_updated":"2023-08-07T07:48:11Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"fb36dda665e57bab006a000bf0faacd5","file_id":"13978","content_type":"application/pdf"}],"abstract":[{"text":"The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","volume":11,"year":"2023","external_id":{"isi":["001038636400001"]},"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863–BORGES. We further thank the office of the Federal Government of Lower Austria, K3-Group–Culture, Science and Education, for their financial support as part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the Electron Microscopy Facility at IST Austria for their support with sputter coating the FO tips and Bernhard Pichler from AIT for software development to facilitate data evaluation.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"oa":1,"publisher":"Frontiers","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"}],"author":[{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"full_name":"Steger-Polt, Marie Helene","last_name":"Steger-Polt","first_name":"Marie Helene"},{"full_name":"Reiner-Rozman, Ciril","first_name":"Ciril","last_name":"Reiner-Rozman"},{"last_name":"Fossati","first_name":"Stefan","full_name":"Fossati, Stefan"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"full_name":"Aspermair, Patrik","first_name":"Patrik","last_name":"Aspermair"},{"full_name":"Kleber, Christoph","first_name":"Christoph","last_name":"Kleber"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"last_name":"Dostalek","first_name":"Jakub","full_name":"Dostalek, Jakub"},{"full_name":"Knoll, Wolfgang","last_name":"Knoll","first_name":"Wolfgang"}],"month":"07","article_number":"1202132","date_created":"2023-08-06T22:01:11Z","day":"14","fulldoi":"https://doi.org/10.3389/fphy.2023.1202132","article_type":"original","file_date_updated":"2023-08-07T07:48:11Z","date_published":"2023-07-14T00:00:00Z","publication_status":"published","scopus_import":"1","quality_controlled":"1","publication_identifier":{"eissn":["2296-424X"]},"citation":{"chicago":"Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” <i>Frontiers in Physics</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fphy.2023.1202132\">https://doi.org/10.3389/fphy.2023.1202132</a>.","short":"R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023).","ista":"Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 11, 1202132.","ama":"Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. <i>Frontiers in Physics</i>. 2023;11. doi:<a href=\"https://doi.org/10.3389/fphy.2023.1202132\">10.3389/fphy.2023.1202132</a>","apa":"Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. <i>Frontiers in Physics</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphy.2023.1202132\">https://doi.org/10.3389/fphy.2023.1202132</a>","mla":"Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” <i>Frontiers in Physics</i>, vol. 11, 1202132, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fphy.2023.1202132\">10.3389/fphy.2023.1202132</a>.","ieee":"R. Hasler <i>et al.</i>, “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” <i>Frontiers in Physics</i>, vol. 11. Frontiers, 2023."},"doi":"10.3389/fphy.2023.1202132","title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","publication":"Frontiers in Physics"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["540"],"citation":{"chicago":"Hasler, Roger, Marie-Helene Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7716920\">https://doi.org/10.5281/ZENODO.7716920</a>.","short":"R. Hasler, M.-H. Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, (2023).","mla":"Hasler, Roger, et al. <i>Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7716920\">10.5281/ZENODO.7716920</a>.","apa":"Hasler, R., Polt, M.-H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7716920\">https://doi.org/10.5281/ZENODO.7716920</a>","ista":"Hasler R, Polt M-H, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7716920\">10.5281/ZENODO.7716920</a>.","ama":"Hasler R, Polt M-H, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7716920\">10.5281/ZENODO.7716920</a>","ieee":"R. Hasler <i>et al.</i>, “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing.” Zenodo, 2023."},"doi":"10.5281/ZENODO.7716920","publisher":"Zenodo","has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.7716920","open_access":"1"}],"title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","type":"research_data_reference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"MaIb"}],"author":[{"full_name":"Hasler, Roger","first_name":"Roger","last_name":"Hasler"},{"full_name":"Polt, Marie-Helene","first_name":"Marie-Helene","last_name":"Polt"},{"last_name":"Reiner-Rozman","first_name":"Ciril","full_name":"Reiner-Rozman, Ciril"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"full_name":"Kleber, Christoph","last_name":"Kleber","first_name":"Christoph"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"full_name":"Dostalek, Jakub","first_name":"Jakub","last_name":"Dostalek"},{"first_name":"Wolfgang","last_name":"Knoll","full_name":"Knoll, Wolfgang"}],"_id":"19308","month":"07","article_processing_charge":"No","date_created":"2025-03-07T08:40:58Z","date_updated":"2026-07-22T06:16:48Z","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13968"}]},"day":"14","OA_type":"green","fulldoi":"https://doi.org/10.5281/ZENODO.7716920","date_published":"2023-07-14T00:00:00Z","abstract":[{"text":"This Dataset contains the raw data from the following publication: \"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: towards improved real-time dual-mode biosensing\" (DOI 10.3389/fphy.2023.1202132)","lang":"eng"}],"oa_version":"Published Version","year":"2023","OA_place":"repository"},{"external_id":{"arxiv":["2311.06103"]},"year":"2023","oa_version":"Preprint","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","text":"A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system's inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL."}],"related_material":{"record":[{"relation":"dissertation_contains","id":"19759","status":"public"}]},"status":"public","date_updated":"2026-07-27T12:47:43Z","article_processing_charge":"No","_id":"15039","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"repository","date_published":"2023-11-10T00:00:00Z","publication_status":"draft","fulldoi":"https://doi.org/10.48550/ARXIV.2311.06103","day":"10","date_created":"2024-02-28T17:59:32Z","month":"11","article_number":"2311.06103","author":[{"last_name":"Prach","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","first_name":"Bernd","full_name":"Prach, Bernd"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"type":"preprint","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication":"arXiv","title":"1-Lipschitz neural networks are more expressive with N-activations","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.06103"}],"doi":"10.48550/ARXIV.2311.06103","arxiv":1,"citation":{"short":"B. Prach, C. Lampert, ArXiv (n.d.).","chicago":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">https://doi.org/10.48550/ARXIV.2311.06103</a>.","ieee":"B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” <i>arXiv</i>. .","mla":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” <i>ArXiv</i>, 2311.06103, doi:<a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">10.48550/ARXIV.2311.06103</a>.","apa":"Prach, B., &#38; Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">https://doi.org/10.48550/ARXIV.2311.06103</a>","ista":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103.","ama":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">10.48550/ARXIV.2311.06103</a>"}},{"doi":"10.1109/cvpr52729.2023.02334","arxiv":1,"publication_identifier":{"eisbn":["9798350301298"],"eissn":["2575-7075"]},"citation":{"ama":"Iofinova EB, Krumes A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2023:24364-24373. doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>","apa":"Iofinova, E. B., Krumes, A., &#38; Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24364–24373). Vancouver, BC, Canada: IEEE. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>","ista":"Iofinova EB, Krumes A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2023, pp. 24364–73, doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>.","ieee":"E. B. Iofinova, A. Krumes, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Vancouver, BC, Canada, 2023, pp. 24364–24373.","chicago":"Iofinova, Eugenia B, Alexandra Krumes, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24364–73. IEEE, 2023. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>.","short":"E.B. Iofinova, A. Krumes, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373."},"publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","title":"Bias in pruned vision models: In-depth analysis and countermeasures","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12622"}],"quality_controlled":"1","publication_status":"published","date_published":"2023-08-22T00:00:00Z","fulldoi":"https://doi.org/10.1109/cvpr52729.2023.02334","day":"22","ec_funded":1,"type":"conference","date_created":"2024-01-10T08:42:40Z","month":"08","author":[{"full_name":"Iofinova, Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","first_name":"Eugenia B","orcid":"0000-0002-7778-3221"},{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"publisher":"IEEE","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","abstract":[{"text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.","lang":"eng"}],"corr_author":"1","isi":1,"project":[{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2023-06-17","end_date":"2023-06-24","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Vancouver, BC, Canada"},"external_id":{"arxiv":["2304.12622"],"isi":["001062531308068"]},"year":"2023","oa_version":"Preprint","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"21854"}],"link":[{"url":"https://github.com/IST-DASLab/pruned-vision-model-bias","relation":"software"}]},"status":"public","date_updated":"2026-07-27T12:50:03Z","article_processing_charge":"No","_id":"14771","page":"24364-24373"}]