[{"status":"public","page":"38187-38206","scopus_import":"1","date_updated":"2024-10-01T08:22:01Z","publication":"Proceedings of the 41st International Conference on Machine Learning","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","intvolume":"       235","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.04679"}],"date_published":"2024-09-01T00:00:00Z","quality_controlled":"1","type":"conference","external_id":{"arxiv":["2401.04679"]},"_id":"18117","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We investigate parameter-efficient fine-tuning (PEFT) methods that can provide good accuracy under limited computational and memory budgets in the context of large language models (LLMs). We present a new PEFT method called Robust Adaptation (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n and highly-sparse components on top of a set of fixed pretrained weights to efficiently approximate the performance of a full-fine-tuning (FFT) solution. Across a series of challenging generative tasks such as grade-school math and SQL query generation, which require fine-tuning for good performance, we show that RoSA outperforms LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter budget, and can even recover the performance of FFT on some tasks. We provide system support for RoSA to complement the training algorithm, specifically in the form of sparse GPU kernels which enable memory- and computationally-efficient training, and show that it is also compatible with low-precision base weights, resulting in the first joint representation combining quantization, low-rank and sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA."}],"citation":{"apa":"Nikdan, M., Tabesh, S., Crncevic, E., &#38; Alistarh, D.-A. (2024). RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 38187–38206). Vienna, Austria: ML Research Press.","mla":"Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 38187–206.","short":"M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 38187–38206.","ieee":"M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient fine-tuning via robust adaptation,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.","chicago":"Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:38187–206. ML Research Press, 2024.","ama":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:38187-38206.","ista":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 235, 38187–38206."},"day":"01","publisher":"ML Research Press","article_processing_charge":"No","corr_author":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/RoSA"}]},"oa":1,"acknowledgement":"The authors would like to thank Eldar Kurtic for experimental support and useful suggestions throughout the project","month":"09","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"author":[{"id":"66374281-f394-11eb-9cf6-869147deecc0","first_name":"Mahdi","full_name":"Nikdan, Mahdi","last_name":"Nikdan"},{"orcid":"0009-0003-4119-6281","first_name":"Soroush","id":"06000900-6068-11ef-8d61-c2472ef2e752","full_name":"Tabesh, Soroush","last_name":"Tabesh"},{"full_name":"Crncevic, Elvir","last_name":"Crncevic","id":"41888001-440d-11ef-8299-d0e838b8185e","first_name":"Elvir"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"volume":235,"arxiv":1,"publication_identifier":{"eissn":["2640-3498"]},"oa_version":"Preprint","date_created":"2024-09-22T22:01:44Z","title":"RoSA: Accurate parameter-efficient fine-tuning via robust adaptation","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","end_date":"2024-07-27","location":"Vienna, Austria"},"publication_status":"published"},{"corr_author":"1","article_processing_charge":"No","publisher":"ML Research Press","author":[{"first_name":"Hossein","id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","full_name":"Zakerinia, Hossein","last_name":"Zakerinia"},{"first_name":"Amin","last_name":"Behjati","full_name":"Behjati, Amin"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"volume":235,"department":[{"_id":"ChLa"}],"month":"09","oa":1,"title":"More flexible PAC-Bayesian meta-learning by learning learning algorithms","date_created":"2024-09-22T22:01:45Z","alternative_title":["PMLR"],"oa_version":"Published Version","publication_identifier":{"eissn":["2640-3498"]},"arxiv":1,"conference":{"location":"Vienna, Austria","end_date":"2024-07-27","start_date":"2024-07-21","name":"ICML: International Conference on Machine Learning"},"publication_status":"published","scopus_import":"1","page":"58122-58139","status":"public","date_updated":"2024-10-01T09:30:03Z","publication":"Proceedings of the 41st International Conference on Machine Learning","date_published":"2024-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2402.04054"}],"intvolume":"       235","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zakerinia, Hossein, et al. “More Flexible PAC-Bayesian Meta-Learning by Learning Learning Algorithms.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 58122–39.","short":"H. Zakerinia, A. Behjati, C. Lampert, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 58122–58139.","ieee":"H. Zakerinia, A. Behjati, and C. Lampert, “More flexible PAC-Bayesian meta-learning by learning learning algorithms,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 58122–58139.","apa":"Zakerinia, H., Behjati, A., &#38; Lampert, C. (2024). More flexible PAC-Bayesian meta-learning by learning learning algorithms. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 58122–58139). Vienna, Austria: ML Research Press.","ama":"Zakerinia H, Behjati A, Lampert C. More flexible PAC-Bayesian meta-learning by learning learning algorithms. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:58122-58139.","ista":"Zakerinia H, Behjati A, Lampert C. 2024. More flexible PAC-Bayesian meta-learning by learning learning algorithms. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 58122–58139.","chicago":"Zakerinia, Hossein, Amin Behjati, and Christoph Lampert. “More Flexible PAC-Bayesian Meta-Learning by Learning Learning Algorithms.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:58122–39. ML Research Press, 2024."},"day":"01","language":[{"iso":"eng"}],"_id":"18118","abstract":[{"text":"We introduce a new framework for studying meta-learning methods using PAC-Bayesian theory. Its main advantage over previous work is that it allows for more flexibility in how the transfer of knowledge between tasks is realized. For previous approaches, this could only happen indirectly, by means of learning prior distributions over models. In contrast, the new generalization bounds that we prove express the process of meta-learning much more directly as learning the learning algorithm that should be used for future tasks. The flexibility of our framework makes it suitable to analyze a wide range of meta-learning mechanisms and even design new mechanisms. Other than our theoretical contributions we also show empirically that our framework improves the prediction quality in practical meta-learning mechanisms.","lang":"eng"}],"external_id":{"arxiv":["2402.04054"]},"type":"conference","quality_controlled":"1"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.04519","open_access":"1"}],"date_published":"2024-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","intvolume":"       235","day":"01","citation":{"mla":"Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 45955–87.","ieee":"A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided debugging for deep neural networks,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.","short":"A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 45955–45987.","apa":"Moakhar, A. S., Iofinova, E. B., Frantar, E., &#38; Alistarh, D.-A. (2024). SPADE: Sparsity-guided debugging for deep neural networks. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 45955–45987). Vienna, Austria: ML Research Press.","ama":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging for deep neural networks. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:45955-45987.","ista":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided debugging for deep neural networks. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 45955–45987.","chicago":"Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:45955–87. ML Research Press, 2024."},"quality_controlled":"1","type":"conference","external_id":{"arxiv":["2310.04519"]},"language":[{"iso":"eng"}],"_id":"18121","abstract":[{"text":"It is known that sparsity can improve interpretability for deep neural networks. However, existing methods in the area either require networks that are pre-trained with sparsity constraints, or impose sparsity after the fact, altering the network’s general behavior. In this paper, we demonstrate, for the first time, that sparsity can instead be incorporated into the interpretation process itself, as a sample-specific preprocessing step. Unlike previous work, this approach, which we call SPADE, does not place constraints on the trained model and does not affect its behavior during inference on the sample. Given a trained model and a target sample, SPADE uses sample-targeted pruning to provide a \"trace\" of the network’s execution on the sample, reducing the network to the most important connections prior to computing an interpretation. We demonstrate that preprocessing with SPADE significantly increases the accuracy of image saliency maps across several interpretability methods. Additionally, SPADE improves the usefulness of neuron visualizations, aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.","lang":"eng"}],"scopus_import":"1","status":"public","page":"45955-45987","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2025-04-25T10:32:05Z","publication":"Proceedings of the 41st International Conference on Machine Learning","oa_version":"Preprint","alternative_title":["PMLR"],"title":"SPADE: Sparsity-guided debugging for deep neural networks","date_created":"2024-09-22T22:01:46Z","arxiv":1,"publication_identifier":{"eissn":["2640-3498"]},"publication_status":"published","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","end_date":"2024-07-27","location":"Vienna, Austria"},"related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/SPADE"}]},"publisher":"ML Research Press","article_processing_charge":"No","corr_author":"1","department":[{"_id":"DaAl"}],"month":"09","project":[{"grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization"}],"author":[{"first_name":"Arshia Soltani","full_name":"Moakhar, Arshia Soltani","last_name":"Moakhar"},{"id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","last_name":"Iofinova"},{"full_name":"Frantar, Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"}],"volume":235,"oa":1,"acknowledgement":"The authors would like to thank Stephen Casper and Tony Wang for their feedback on this work, and Eldar Kurtic for his advice on aspects of the project. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35."},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"year":"2024","intvolume":"     14933","date_published":"2024-09-11T00:00:00Z","quality_controlled":"1","type":"conference","external_id":{"arxiv":["2403.05386"],"isi":["001336893300031"]},"abstract":[{"text":"We study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools.","lang":"eng"}],"_id":"18155","language":[{"iso":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Ehsan Goharshady, Mehrdad Karrabi, and Dorde Zikelic. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 14933:600–619. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">https://doi.org/10.1007/978-3-031-71162-6_31</a>.","ama":"Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 14933. Springer Nature; 2024:600-619. doi:<a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">10.1007/978-3-031-71162-6_31</a>","ista":"Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. 2024. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). FM: Formal Methods, LNCS, vol. 14933, 600–619.","apa":"Chatterjee, K., Goharshady, A. K., Goharshady, E., Karrabi, M., &#38; Zikelic, D. (2024). Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 14933, pp. 600–619). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">https://doi.org/10.1007/978-3-031-71162-6_31</a>","mla":"Chatterjee, Krishnendu, et al. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 14933, Springer Nature, 2024, pp. 600–19, doi:<a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">10.1007/978-3-031-71162-6_31</a>.","ieee":"K. Chatterjee, A. K. Goharshady, E. Goharshady, M. Karrabi, and D. Zikelic, “Sound and complete witnesses for template-based verification of LTL properties on polynomial programs,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Milan, Italy, 2024, vol. 14933, pp. 600–619.","short":"K. Chatterjee, A.K. Goharshady, E. Goharshady, M. Karrabi, D. Zikelic, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp. 600–619."},"day":"11","has_accepted_license":"1","status":"public","page":"600-619","scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2024-10-01T09:56:54Z","isi":1,"date_updated":"2025-09-08T09:51:34Z","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","publication_identifier":{"isbn":["9783031711619"],"issn":["0302-9743"],"eissn":["1611-3349"]},"arxiv":1,"oa_version":"Published Version","title":"Sound and complete witnesses for template-based verification of LTL properties on polynomial programs","date_created":"2024-09-29T22:01:37Z","alternative_title":["LNCS"],"conference":{"name":"FM: Formal Methods","start_date":"2024-09-09","end_date":"2024-09-13","location":"Milan, Italy"},"publication_status":"published","file":[{"file_name":"2024_LNCS_Chatterjee.pdf","checksum":"223845be9e754681ee218866827c95e7","creator":"dernst","file_id":"18165","date_updated":"2024-10-01T09:56:54Z","relation":"main_file","access_level":"open_access","file_size":650495,"date_created":"2024-10-01T09:56:54Z","success":1,"content_type":"application/pdf"}],"publisher":"Springer Nature","article_processing_charge":"Yes (in subscription journal)","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1007/978-3-031-71162-6_31","oa":1,"acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Hong Kong Research Grants Council ECS Project Number 26208122.","month":"09","department":[{"_id":"KrCh"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Ehsan","last_name":"Goharshady","full_name":"Goharshady, Ehsan"},{"id":"67638922-f394-11eb-9cf6-f20423e08757","first_name":"Mehrdad","full_name":"Karrabi, Mehrdad","last_name":"Karrabi"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"volume":14933},{"day":"01","citation":{"mla":"Akshay, S., et al. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties,” in <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, Jeju, Korea, 2024, pp. 3–12.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2024). Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i> (pp. 3–12). Jeju, Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In: <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:3-12. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2024. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 3–12.","chicago":"Akshay, S, Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, 3–12. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>."},"_id":"18159","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a classical model for decision making in the presence of uncertainty. Often they are viewed as state transformers with planning objectives defned with respect to paths over MDP states. An increasingly\r\npopular alternative is to view them as distribution transformers, giving rise to a sequence of probability distributions over MDP states. For instance, reachability and safety properties in modeling robot swarms or chemical reaction networks are naturally defned in terms of probability distributions over states. Verifying such distributional properties is known to be hard and often beyond the reach of classical state-based verifcation techniques. In this work, we consider the problems of certifed policy (i.e. controller) verifcation and synthesis in MDPs under distributional reach-avoidance specifcations. By certifed we mean that, along with a policy, we also aim to synthesize a (checkable) certifcate ensuring that the MDP indeed satisfes the property. Thus, given the target set of distributions and an unsafe set of distributions over MDP states, our goal is to either synthesize a certifcate for a given policy or synthesize a policy along with a certifcate, proving that the target distribution can be reached while avoiding unsafe distributions. To solve this problem, we introduce the novel notion of distributional reach-avoid certifcates and present automated procedures for (1) synthesizing a certifcate for a given policy, and (2) synthesizing a policy together with the certifcate, both providing formal guarantees on certifcate correctness. Our experimental evaluation demonstrates the ability of our method to solve several non-trivial examples, including a multi-agent robot-swarm model, to synthesize certifed policies and to certify existing policies. "}],"external_id":{"arxiv":["2405.04015"]},"type":"conference","quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.04015"}],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence","date_updated":"2025-04-14T07:52:46Z","ec_funded":1,"scopus_import":"1","page":"3-12","status":"public","publication_status":"published","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2024-08-03","end_date":"2024-08-09","location":"Jeju, Korea"},"title":"Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties","date_created":"2024-09-29T22:01:38Z","oa_version":"Preprint","publication_identifier":{"issn":["1045-0823"],"isbn":["9781956792041"]},"arxiv":1,"author":[{"first_name":"S","full_name":"Akshay, S","last_name":"Akshay"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"department":[{"_id":"KrCh"}],"month":"09","acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt), the Singapore Ministry of Education (MOE) Academic Research Fund (AcRF) Tier 1 grant, Google Research Award 2023 and the SBI Foundation Hub for Data and Analytics.","oa":1,"doi":"10.24963/ijcai.2024/1","corr_author":"1","article_processing_charge":"No","publisher":"International Joint Conferences on Artificial Intelligence"},{"publication_status":"published","conference":{"start_date":"2024-08-03","name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Jeju, South Korea","end_date":"2024-08-09"},"arxiv":1,"publication_identifier":{"isbn":["9781956792041"],"issn":["1045-0823"]},"OA_type":"green","oa_version":"Preprint","title":"Solving long-run average reward robust MDPs via stochastic games","date_created":"2024-09-29T22:01:39Z","oa":1,"doi":"10.24963/ijcai.2024/741","acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Czech Science Foundation\r\ngrant no. GA23-06963S.","department":[{"_id":"KrCh"}],"month":"09","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Kafshdar Goharshadi","full_name":"Kafshdar Goharshadi, Ehsan","first_name":"Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","orcid":"0000-0002-8595-0587"},{"first_name":"Mehrdad","id":"67638922-f394-11eb-9cf6-f20423e08757","last_name":"Karrabi","full_name":"Karrabi, Mehrdad"},{"last_name":"Novotný","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"publisher":"International Joint Conferences on Artificial Intelligence","article_processing_charge":"No","corr_author":"1","quality_controlled":"1","type":"conference","external_id":{"arxiv":["2312.13912"]},"language":[{"iso":"eng"}],"_id":"18160","abstract":[{"text":"Markov decision processes (MDPs) provide a standard framework for sequential decision making under uncertainty. However, MDPs do not take uncertainty in transition probabilities into account. Robust Markov decision processes (RMDPs) address this shortcoming of MDPs by assigning to each transition an uncertainty set rather than a single probability value. In this work, we consider polytopic RMDPs in which all uncertainty sets are polytopes and study the problem of solving long-run average reward polytopic RMDPs. We present a novel perspective on this problem and show that it can be reduced to solving long-run average reward turn-based stochastic games with finite state and action spaces. This reduction allows us to derive several important consequences that were hitherto not known to hold for polytopic RMDPs. First, we derive new computational complexity bounds for solving long-run average reward polytopic RMDPs, showing for the first time that the threshold decision problem for them is in NP∩CONP and that they admit a randomized algorithm with sub-exponential expected runtime. Second, we present Robust Polytopic Policy Iteration (RPPI), a novel policy iteration algorithm for solving long-run average reward polytopic RMDPs. Our experimental evaluation shows that RPPI is much more efficient in solving long-run average reward polytopic RMDPs compared to state-of-the-art methods based on value iteration. ","lang":"eng"}],"day":"01","citation":{"apa":"Chatterjee, K., Goharshady, E., Karrabi, M., Novotný, P., &#38; Zikelic, D. (2024). Solving long-run average reward robust MDPs via stochastic games. In <i>33rd International Joint Conference on Artificial Intelligence</i> (pp. 6707–6715). Jeju, South Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>","ieee":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, and D. Zikelic, “Solving long-run average reward robust MDPs via stochastic games,” in <i>33rd International Joint Conference on Artificial Intelligence</i>, Jeju, South Korea, 2024, pp. 6707–6715.","short":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, D. Zikelic, in:, 33rd International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–6715.","mla":"Chatterjee, Krishnendu, et al. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” <i>33rd International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–15, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Mehrdad Karrabi, Petr Novotný, and Dorde Zikelic. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” In <i>33rd International Joint Conference on Artificial Intelligence</i>, 6707–15. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>.","ista":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. 2024. Solving long-run average reward robust MDPs via stochastic games. 33rd International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 6707–6715.","ama":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. Solving long-run average reward robust MDPs via stochastic games. In: <i>33rd International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:6707-6715. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.13912","open_access":"1"}],"OA_place":"repository","date_published":"2024-09-01T00:00:00Z","publication":"33rd International Joint Conference on Artificial Intelligence","date_updated":"2025-04-14T07:52:46Z","page":"6707-6715","status":"public","scopus_import":"1","ec_funded":1},{"doi":"10.1038/s41422-024-01035-x","article_type":"original","department":[{"_id":"JiFr"}],"month":"11","volume":34,"author":[{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"publisher":"Springer Nature","corr_author":"1","article_processing_charge":"No","pmid":1,"publication_status":"published","publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"oa_version":"None","OA_type":"closed access","title":"Feeling the danger: Local wound signaling in plants","date_created":"2024-10-13T22:01:51Z","isi":1,"publication":"Cell Research","date_updated":"2025-09-08T09:57:18Z","page":"761-762","status":"public","scopus_import":"1","type":"journal_article","quality_controlled":"1","_id":"18311","abstract":[{"text":"Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001326684200001"],"pmid":["39354142"]},"day":"01","citation":{"ama":"Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. 2024;34:761-762. doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>","ista":"Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants. Cell Research. 34, 761–762.","chicago":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>.","mla":"Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling in Plants.” <i>Cell Research</i>, vol. 34, Springer Nature, 2024, pp. 761–62, doi:<a href=\"https://doi.org/10.1038/s41422-024-01035-x\">10.1038/s41422-024-01035-x</a>.","ieee":"L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,” <i>Cell Research</i>, vol. 34. Springer Nature, pp. 761–762, 2024.","short":"L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762.","apa":"Hörmayer, L., &#38; Friml, J. (2024). Feeling the danger: Local wound signaling in plants. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-024-01035-x\">https://doi.org/10.1038/s41422-024-01035-x</a>"},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        34","date_published":"2024-11-01T00:00:00Z"},{"OA_type":"gold","oa_version":"Published Version","date_created":"2024-10-20T22:02:05Z","title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","publication_identifier":{"eissn":["2041-1723"]},"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2024-10-21T12:15:38Z","file_size":7215329,"checksum":"03d6dd1b84efa24e9e9ede748d08764d","file_name":"2024_NatureComm_Zupancic.pdf","file_id":"18460","date_updated":"2024-10-21T12:15:38Z","creator":"dernst","relation":"main_file"}],"publication_status":"published","pmid":1,"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"10","department":[{"_id":"RySh"}],"article_type":"original","author":[{"full_name":"Zupančič, Maja","last_name":"Zupančič","first_name":"Maja"},{"last_name":"Keimpema","full_name":"Keimpema, Erik","first_name":"Erik"},{"first_name":"Evgenii O.","last_name":"Tretiakov","full_name":"Tretiakov, Evgenii O."},{"first_name":"Stephanie J.","full_name":"Eder, Stephanie J.","last_name":"Eder"},{"first_name":"Itamar","full_name":"Lev, Itamar","last_name":"Lev"},{"first_name":"Lukas","full_name":"Englmaier, Lukas","last_name":"Englmaier"},{"orcid":"0000-0003-0863-4481","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep"},{"full_name":"Fietz, Simone A.","last_name":"Fietz","first_name":"Simone A."},{"last_name":"Härtig","full_name":"Härtig, Wolfgang","first_name":"Wolfgang"},{"last_name":"Renaux","full_name":"Renaux, Estelle","first_name":"Estelle"},{"first_name":"Andreas","full_name":"Villunger, Andreas","last_name":"Villunger"},{"first_name":"Tomas","full_name":"Hökfelt, Tomas","last_name":"Hökfelt"},{"first_name":"Manuel","full_name":"Zimmer, Manuel","last_name":"Zimmer"},{"full_name":"Clotman, Frédéric","last_name":"Clotman","first_name":"Frédéric"},{"last_name":"Harkany","full_name":"Harkany, Tibor","first_name":"Tibor"}],"volume":15,"oa":1,"doi":"10.1038/s41467-024-52762-z","acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute.","OA_place":"publisher","date_published":"2024-10-05T00:00:00Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","intvolume":"        15","article_number":"8631","day":"05","citation":{"chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>.","ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>","apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>","ieee":"M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024).","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>."},"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"pmid":["39366958"],"isi":["001409493300014"]},"language":[{"iso":"eng"}],"_id":"18445","abstract":[{"lang":"eng","text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus."}],"scopus_import":"1","DOAJ_listed":"1","status":"public","PlanS_conform":"1","isi":1,"publication":"Nature Communications","date_updated":"2025-09-08T14:25:06Z","file_date_updated":"2024-10-21T12:15:38Z"},{"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"oa_version":"Submitted Version","OA_type":"green","date_created":"2024-10-20T22:02:06Z","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","doi":"10.1126/science.adh1145","oa":1,"article_type":"original","month":"10","department":[{"_id":"EdHa"}],"volume":386,"author":[{"first_name":"Dimitri","full_name":"Fabrèges, Dimitri","last_name":"Fabrèges"},{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","orcid":"0000-0001-9806-5643"},{"last_name":"Moghe","full_name":"Moghe, Prachiti","first_name":"Prachiti"},{"last_name":"Kickuth","full_name":"Kickuth, Alison","first_name":"Alison"},{"first_name":"Takafumi","full_name":"Ichikawa, Takafumi","last_name":"Ichikawa"},{"first_name":"Chizuru","last_name":"Iwatani","full_name":"Iwatani, Chizuru"},{"first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki","last_name":"Tsukiyama"},{"first_name":"Nathalie","last_name":"Daniel","full_name":"Daniel, Nathalie"},{"first_name":"Julie","last_name":"Gering","full_name":"Gering, Julie"},{"first_name":"Anniek","last_name":"Stokkermans","full_name":"Stokkermans, Anniek"},{"last_name":"Wolny","full_name":"Wolny, Adrian","first_name":"Adrian"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"last_name":"Duranthon","full_name":"Duranthon, Véronique","first_name":"Véronique"},{"first_name":"Virginie","last_name":"Uhlman","full_name":"Uhlman, Virginie"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Hiiragi, Takashi","last_name":"Hiiragi","first_name":"Takashi"}],"publisher":"AAAS","corr_author":"1","article_processing_charge":"No","pmid":1,"type":"journal_article","quality_controlled":"1","_id":"18446","language":[{"iso":"eng"}],"abstract":[{"text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.","lang":"eng"}],"external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"day":"11","citation":{"ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. 2024;386(6718). doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>.","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:<a href=\"https://doi.org/10.1126/science.adh1145\">10.1126/science.adh1145</a>.","ieee":"D. Fabrèges <i>et al.</i>, “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” <i>Science</i>, vol. 386, no. 6718. AAAS, 2024.","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adh1145\">https://doi.org/10.1126/science.adh1145</a>"},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"eadh1145","intvolume":"       386","main_file_link":[{"url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf","open_access":"1"}],"date_published":"2024-10-11T00:00:00Z","OA_place":"repository","isi":1,"publication":"Science","date_updated":"2025-09-08T14:22:13Z","status":"public","scopus_import":"1","issue":"6718"},{"file":[{"access_level":"open_access","file_size":3675955,"date_created":"2025-01-13T09:20:15Z","success":1,"content_type":"application/pdf","file_name":"2024_DevelopmentalCell_Janacek.pdf","checksum":"34423ee9fb4e30334f3572eddf1da2ae","creator":"dernst","date_updated":"2025-01-13T09:20:15Z","relation":"main_file","file_id":"18835"}],"publication_status":"published","date_created":"2024-10-23T08:41:27Z","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","oa_version":"Published Version","OA_type":"hybrid","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"author":[{"full_name":"Janacek, DP","last_name":"Janacek","first_name":"DP"},{"first_name":"M","full_name":"Kolb, M","last_name":"Kolb"},{"last_name":"Schulz","full_name":"Schulz, L","first_name":"L"},{"full_name":"Mergner, J","last_name":"Mergner","first_name":"J"},{"first_name":"B","full_name":"Kuster, B","last_name":"Kuster"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"K","last_name":"Ten Tusscher","full_name":"Ten Tusscher, K"},{"last_name":"Schwechheimer","full_name":"Schwechheimer, C","first_name":"C"},{"first_name":"UZ","full_name":"Hammes, UZ","last_name":"Hammes"}],"volume":59,"article_type":"original","month":"12","department":[{"_id":"JiFr"}],"acknowledgement":"This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions.","doi":"10.1016/j.devcel.2024.09.020","oa":1,"pmid":1,"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","has_accepted_license":"1","day":"16","citation":{"ista":"Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0.","ama":"Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. 2024;59(14):S1534-5807(24)00569-0. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>","chicago":"Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>.","short":"D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.","ieee":"D. Janacek <i>et al.</i>, “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” <i>Developmental Cell</i>, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.","mla":"Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental Cell</i>, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">10.1016/j.devcel.2024.09.020</a>.","apa":"Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.09.020\">https://doi.org/10.1016/j.devcel.2024.09.020</a>"},"language":[{"iso":"eng"}],"_id":"18465","abstract":[{"text":"The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.","lang":"eng"}],"external_id":{"isi":["001390774300001"],"pmid":["39413780"]},"type":"journal_article","quality_controlled":"1","date_published":"2024-12-16T00:00:00Z","OA_place":"publisher","intvolume":"        59","year":"2024","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Developmental Cell","date_updated":"2025-09-08T14:33:17Z","isi":1,"file_date_updated":"2025-01-13T09:20:15Z","issue":"14","license":"https://creativecommons.org/licenses/by-nc/4.0/","scopus_import":"1","status":"public","page":"S1534-5807(24)00569-0"},{"has_accepted_license":"1","citation":{"ama":"Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>","ista":"Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.","chicago":"Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>.","mla":"Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.040311\">10.1103/prxquantum.5.040311</a>.","short":"M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).","ieee":"M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>, vol. 5, no. 4. American Physical Society, 2024.","apa":"Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.040311\">https://doi.org/10.1103/prxquantum.5.040311</a>"},"day":"23","_id":"18488","abstract":[{"lang":"eng","text":"The advancement of quantum simulators motivates the development of a theoretical framework to assist with efficient state preparation in quantum many-body systems. Generally, preparing a target entangled state via unitary evolution with time-dependent couplings is a challenging task and very little is known about the existence of solutions and their properties. In this work we develop a constructive approach for preparing matrix product states (MPS) via continuous unitary evolution. We provide an explicit construction of the operator that exactly implements the evolution of a given MPS along a specified direction in its tangent space. This operator can be written as a sum of local terms of finite range, yet it is in general non-Hermitian. Relying on the explicit construction of the non-Hermitian generator of the dynamics, we demonstrate the existence of a Hermitian sequence of operators that implements the desired MPS evolution with an error that decreases exponentially with the operator range. The construction is benchmarked on an explicit periodic trajectory in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary generating the dynamics over one period of the trajectory features an approximate MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results show that our construction is not only useful for state preparation and control of many-body systems, but also provides a generic route towards Floquet scars—periodically driven models with quasilocal generators of dynamics that have exact MPS eigenstates in their spectrum."}],"language":[{"iso":"eng"}],"external_id":{"isi":["001346198800001"],"arxiv":["2403.12325"]},"type":"journal_article","quality_controlled":"1","date_published":"2024-10-23T00:00:00Z","APC_amount":"3711,01 EUR","OA_place":"publisher","intvolume":"         5","article_number":"040311","year":"2024","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"PRX Quantum","date_updated":"2025-09-08T14:26:29Z","isi":1,"file_date_updated":"2024-10-30T08:59:09Z","issue":"4","ec_funded":1,"DOAJ_listed":"1","scopus_import":"1","status":"public","file":[{"date_updated":"2024-10-30T08:59:09Z","creator":"dernst","file_id":"18489","relation":"main_file","checksum":"2e057ba021744d0a74602517935326b3","file_name":"2024_PRXQuantum_Ljubotina.pdf","success":1,"content_type":"application/pdf","date_created":"2024-10-30T08:59:09Z","file_size":1151431,"access_level":"open_access"}],"publication_status":"published","title":"Tangent space generators of matrix product states and exact floquet quantum scars","date_created":"2024-10-29T16:04:05Z","oa_version":"Published Version","OA_type":"gold","arxiv":1,"publication_identifier":{"eissn":["2691-3399"]},"author":[{"orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","full_name":"Ljubotina, Marko","last_name":"Ljubotina"},{"last_name":"Petrova","full_name":"Petrova, Elena","first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"full_name":"Schuch, Norbert","last_name":"Schuch","first_name":"Norbert"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"volume":5,"article_type":"original","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"department":[{"_id":"MaSe"}],"month":"10","acknowledgement":"We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions. This research was funded in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1, 10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This work was performed in part at the Aspen Center for Physics, which is supported by National Science Foundation Grant PHY-2210452. This research was supported in part by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","oa":1,"doi":"10.1103/prxquantum.5.040311","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","article_processing_charge":"Yes","publisher":"American Physical Society"},{"author":[{"last_name":"Bonakdarpour","full_name":"Bonakdarpour, Borzoo","first_name":"Borzoo"},{"full_name":"Momtaz, Anik","last_name":"Momtaz","first_name":"Anik"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","full_name":"Sarac, Naci E","last_name":"Sarac"}],"volume":15191,"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"month":"10","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"}],"oa":1,"doi":"10.1007/978-3-031-74234-7_18","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Springer Nature","file":[{"checksum":"7b8ca21b8c19ab796fa445b0e54003ca","file_name":"2024_LNCS_Bonakdarpour.pdf","creator":"dernst","relation":"main_file","file_id":"18539","date_updated":"2024-11-11T09:42:28Z","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2024-11-11T09:42:28Z","file_size":1897101}],"conference":{"end_date":"2024-10-17","location":"Istanbul, Turkey","name":"RV: Conference on Runtime Verification","start_date":"2024-10-15"},"publication_status":"published","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","alternative_title":["LNCS"],"date_created":"2024-11-10T23:01:58Z","OA_type":"hybrid","oa_version":"Published Version","arxiv":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031742330"]},"publication":"24th International Conference on Runtime Verification","date_updated":"2025-09-08T14:39:14Z","isi":1,"file_date_updated":"2024-11-11T09:42:28Z","ec_funded":1,"scopus_import":"1","page":"282-301","status":"public","day":"12","citation":{"mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>.","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>","ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>."},"has_accepted_license":"1","external_id":{"isi":["001420093700018"],"arxiv":["2408.05033"]},"abstract":[{"text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples.","lang":"eng"}],"_id":"18521","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","OA_place":"publisher","date_published":"2024-10-12T00:00:00Z","APC_amount":"2290 EUR","intvolume":"     15191","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024"},{"publication_status":"published","file":[{"success":1,"content_type":"application/pdf","date_created":"2024-11-11T08:32:02Z","file_size":563394,"access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"18532","date_updated":"2024-11-11T08:32:02Z","checksum":"26826786a960039b9501cfc5cb4f3fe6","file_name":"2024_LMCS_Bose.pdf"}],"arxiv":1,"publication_identifier":{"eissn":["1860-5974"]},"date_created":"2024-11-10T23:02:01Z","title":"History-deterministic timed automata","oa_version":"Published Version","OA_type":"gold","acknowledgement":"This work has in parts been presented at the 33rd International Conference on Concurrency Theory (CONCUR’22) [HLT22] and at the 16th International Workshop on Reachability Problems (RP’22) [BHL+22]. This work was supported by the EU (ERC-2020-AdG 101020093); the EPSRC (EP/V025848/1, EP/X042596/1, EP/X017796/1 and EP/X03688X/1); and the ANR (QUASY 23-CE48-0008-01).","doi":"10.46298/lmcs-20(4:1)2024","oa":1,"volume":20,"author":[{"last_name":"Bose","full_name":"Bose, Sougata","first_name":"Sougata"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"first_name":"Karoliina","last_name":"Lehtinen","full_name":"Lehtinen, Karoliina"},{"full_name":"Schewe, Sven","last_name":"Schewe","first_name":"Sven"},{"last_name":"Totzke","full_name":"Totzke, Patrick","first_name":"Patrick"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"article_type":"original","department":[{"_id":"ToHe"}],"month":"10","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"EPI Sciences","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12508"}]},"abstract":[{"text":"We explore the notion of history-determinism in the context of timed automata (TA) over infinite timed words. History-deterministic (HD) automata are those in which nondeterminism can be resolved on the fly, based on the run constructed thus far. History-determinism is a robust property that admits different game-based characterisations, and HD specifications allow for game-based verification without an expensive determinization step. We show that the class of timed ω\r\n-languages recognized by HD timed automata strictly extends that of deterministic ones, and is strictly included in those recognised by fully non-deterministic TA. For non-deterministic timed automata it is known that universality is already undecidable for safety/reachability TA. For history-deterministic TA with arbitrary parity acceptance, we show that timed universality, inclusion, and synthesis all remain decidable and are EXPTIME-complete. For the subclass of TA with safety or reachability acceptance, one can decide (in EXPTIME) whether such an automaton is history-deterministic. If so, it can effectively determinized without introducing new automaton states.","lang":"eng"}],"_id":"18530","language":[{"iso":"eng"}],"external_id":{"arxiv":["2304.03183"],"isi":["001332466900002"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","day":"02","citation":{"apa":"Bose, S., Henzinger, T. A., Lehtinen, K., Schewe, S., &#38; Totzke, P. (2024). History-deterministic timed automata. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-20(4:1)2024\">https://doi.org/10.46298/lmcs-20(4:1)2024</a>","mla":"Bose, Sougata, et al. “History-Deterministic Timed Automata.” <i>Logical Methods in Computer Science</i>, vol. 20, no. 4, EPI Sciences, 2024, pp. 1–28, doi:<a href=\"https://doi.org/10.46298/lmcs-20(4:1)2024\">10.46298/lmcs-20(4:1)2024</a>.","ieee":"S. Bose, T. A. Henzinger, K. Lehtinen, S. Schewe, and P. Totzke, “History-deterministic timed automata,” <i>Logical Methods in Computer Science</i>, vol. 20, no. 4. EPI Sciences, pp. 1–28, 2024.","short":"S. Bose, T.A. Henzinger, K. Lehtinen, S. Schewe, P. Totzke, Logical Methods in Computer Science 20 (2024) 1–28.","chicago":"Bose, Sougata, Thomas A Henzinger, Karoliina Lehtinen, Sven Schewe, and Patrick Totzke. “History-Deterministic Timed Automata.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2024. <a href=\"https://doi.org/10.46298/lmcs-20(4:1)2024\">https://doi.org/10.46298/lmcs-20(4:1)2024</a>.","ama":"Bose S, Henzinger TA, Lehtinen K, Schewe S, Totzke P. History-deterministic timed automata. <i>Logical Methods in Computer Science</i>. 2024;20(4):1-28. doi:<a href=\"https://doi.org/10.46298/lmcs-20(4:1)2024\">10.46298/lmcs-20(4:1)2024</a>","ista":"Bose S, Henzinger TA, Lehtinen K, Schewe S, Totzke P. 2024. History-deterministic timed automata. Logical Methods in Computer Science. 20(4), 1–28."},"intvolume":"        20","year":"2024","ddc":["000"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-02T00:00:00Z","OA_place":"publisher","file_date_updated":"2024-11-11T08:32:02Z","date_updated":"2025-09-08T14:35:17Z","publication":"Logical Methods in Computer Science","isi":1,"status":"public","page":"1-28","issue":"4","DOAJ_listed":"1","ec_funded":1,"scopus_import":"1"},{"date_published":"2024-12-19T00:00:00Z","OA_place":"publisher","intvolume":"        84","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"has_accepted_license":"1","citation":{"chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>","ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12."},"day":"19","abstract":[{"lang":"eng","text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component."}],"_id":"18553","language":[{"iso":"eng"}],"external_id":{"isi":["001395711300001"],"pmid":["39547223"]},"type":"journal_article","quality_controlled":"1","issue":"24","scopus_import":"1","page":"4740-4757.e12","status":"public","date_updated":"2025-09-08T14:42:50Z","publication":"Molecular Cell","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"isi":1,"file_date_updated":"2025-01-13T11:17:35Z","title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","date_created":"2024-11-15T12:12:54Z","oa_version":"Published Version","OA_type":"hybrid","publication_identifier":{"issn":["1097-2765"]},"file":[{"date_updated":"2025-01-13T11:17:35Z","file_id":"18844","relation":"main_file","creator":"dernst","file_name":"2024_MolecularCell_Ramadhin.pdf","checksum":"e051e2766b2d424983778f742cb7c5ed","date_created":"2025-01-13T11:17:35Z","file_size":25071994,"success":1,"content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","pmid":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Elsevier","author":[{"full_name":"Ramadhin, Anisha R.","last_name":"Ramadhin","first_name":"Anisha R."},{"first_name":"Shun-Hsiao","last_name":"Lee","full_name":"Lee, Shun-Hsiao"},{"first_name":"Di","full_name":"Zhou, Di","last_name":"Zhou"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"first_name":"Camila","last_name":"Gonzalo-Hansen","full_name":"Gonzalo-Hansen, Camila"},{"first_name":"Marjolein","full_name":"van Sluis, Marjolein","last_name":"van Sluis"},{"first_name":"Cindy M.A.","last_name":"Blom","full_name":"Blom, Cindy M.A."},{"first_name":"Roel C.","full_name":"Janssens, Roel C.","last_name":"Janssens"},{"full_name":"Raams, Anja","last_name":"Raams","first_name":"Anja"},{"first_name":"Dick","last_name":"Dekkers","full_name":"Dekkers, Dick"},{"full_name":"Bezstarosti, Karel","last_name":"Bezstarosti","first_name":"Karel"},{"full_name":"Slade, Dea","last_name":"Slade","first_name":"Dea"},{"first_name":"Wim","full_name":"Vermeulen, Wim","last_name":"Vermeulen"},{"last_name":"Pines","full_name":"Pines, Alex","first_name":"Alex"},{"full_name":"Demmers, Jeroen A.A.","last_name":"Demmers","first_name":"Jeroen A.A."},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A"},{"first_name":"Titia K.","last_name":"Sixma","full_name":"Sixma, Titia K."},{"full_name":"Marteijn, Jurgen A.","last_name":"Marteijn","first_name":"Jurgen A."}],"volume":84,"article_type":"original","month":"12","department":[{"_id":"CaBe"}],"acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","oa":1,"doi":"10.1016/j.molcel.2024.10.030"},{"file":[{"content_type":"application/pdf","success":1,"date_created":"2024-11-18T07:49:25Z","file_size":908541,"access_level":"open_access","file_id":"18560","date_updated":"2024-11-18T07:49:25Z","relation":"main_file","creator":"dernst","checksum":"5f9b35e115c3d375e99be78da9054cb4","file_name":"2024_LIPIcs_CultreradiMontesano.pdf"}],"conference":{"start_date":"2024-09-18","name":"GD: Graph Drawing and Network Visualization","location":"Vienna, Austria","end_date":"2024-09-20"},"publication_status":"published","oa_version":"Published Version","OA_type":"gold","title":"The Euclidean MST-ratio for bi-colored lattices","date_created":"2024-11-17T23:01:47Z","alternative_title":["LIPIcs"],"arxiv":1,"publication_identifier":{"isbn":["9783959773430"],"issn":["1868-8969"]},"project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"month":"10","department":[{"_id":"HeEd"}],"volume":320,"author":[{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"full_name":"Draganov, Ondrej","last_name":"Draganov","first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0464-3823"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, \"Discretization in Geometry and Dynamics\", Austrian Science Fund (FWF), grant no. I 02979-N35.","doi":"10.4230/LIPIcs.GD.2024.3","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","article_processing_charge":"Yes","has_accepted_license":"1","citation":{"apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2024). The Euclidean MST-ratio for bi-colored lattices. In <i>32nd International Symposium on Graph Drawing and Network Visualization</i> (Vol. 320). Vienna, Austria: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>","mla":"Cultrera di Montesano, Sebastiano, et al. “The Euclidean MST-Ratio for Bi-Colored Lattices.” <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, vol. 320, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, in:, 32nd International Symposium on Graph Drawing and Network Visualization, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “The Euclidean MST-ratio for bi-colored lattices,” in <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vienna, Austria, 2024, vol. 320.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “The Euclidean MST-Ratio for Bi-Colored Lattices.” In <i>32nd International Symposium on Graph Drawing and Network Visualization</i>, Vol. 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">https://doi.org/10.4230/LIPIcs.GD.2024.3</a>.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. The Euclidean MST-ratio for bi-colored lattices. In: <i>32nd International Symposium on Graph Drawing and Network Visualization</i>. Vol 320. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.GD.2024.3\">10.4230/LIPIcs.GD.2024.3</a>","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2024. The Euclidean MST-ratio for bi-colored lattices. 32nd International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LIPIcs, vol. 320, 3."},"day":"28","type":"conference","quality_controlled":"1","_id":"18556","abstract":[{"text":"Given a finite set, A ⊆ ℝ², and a subset, B ⊆ A, the MST-ratio is the combined length of the minimum spanning trees of B and A⧵B divided by the length of the minimum spanning tree of A. The question of the supremum, over all sets A, of the maximum, over all subsets B, is related to the Steiner ratio, and we prove this sup-max is between 2.154 and 2.427. Restricting ourselves to 2-dimensional lattices, we prove that the sup-max is 2, while the inf-max is 1.25. By some margin the most difficult of these results is the upper bound for the inf-max, which we prove by showing that the hexagonal lattice cannot have MST-ratio larger than 1.25.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2403.10204"],"isi":["001540278400001"]},"date_published":"2024-10-28T00:00:00Z","OA_place":"publisher","year":"2024","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3","intvolume":"       320","isi":1,"publication":"32nd International Symposium on Graph Drawing and Network Visualization","date_updated":"2025-12-02T13:50:50Z","file_date_updated":"2024-11-18T07:49:25Z","scopus_import":"1","ec_funded":1,"status":"public"},{"scopus_import":"1","editor":[{"first_name":"Susanne","last_name":"Graf","full_name":"Graf, Susanne"},{"first_name":"Paul","full_name":"Pettersson, Paul","last_name":"Pettersson"},{"first_name":"Bernhard","full_name":"Steffen, Bernhard","last_name":"Steffen"}],"page":"154-164","status":"public","date_updated":"2025-08-05T12:19:50Z","publication":"Real Time and Such","date_published":"2024-10-23T00:00:00Z","intvolume":"     15230","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","citation":{"mla":"Henzinger, Thomas A. “Reminiscences of a Real-Time Researcher.” <i>Real Time and Such</i>, edited by Susanne Graf et al., vol. 15230, Springer Nature, 2024, pp. 154–64, doi:<a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">10.1007/978-3-031-73751-0_12</a>.","short":"T.A. Henzinger, in:, S. Graf, P. Pettersson, B. Steffen (Eds.), Real Time and Such, Springer Nature, Cham, 2024, pp. 154–164.","ieee":"T. A. Henzinger, “Reminiscences of a Real-Time Researcher,” in <i>Real Time and Such</i>, vol. 15230, S. Graf, P. Pettersson, and B. Steffen, Eds. Cham: Springer Nature, 2024, pp. 154–164.","apa":"Henzinger, T. A. (2024). Reminiscences of a Real-Time Researcher. In S. Graf, P. Pettersson, &#38; B. Steffen (Eds.), <i>Real Time and Such</i> (Vol. 15230, pp. 154–164). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">https://doi.org/10.1007/978-3-031-73751-0_12</a>","ama":"Henzinger TA. Reminiscences of a Real-Time Researcher. In: Graf S, Pettersson P, Steffen B, eds. <i>Real Time and Such</i>. Vol 15230. LNCS. Cham: Springer Nature; 2024:154-164. doi:<a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">10.1007/978-3-031-73751-0_12</a>","ista":"Henzinger TA. 2024.Reminiscences of a Real-Time Researcher. In: Real Time and Such. LNCS, vol. 15230, 154–164.","chicago":"Henzinger, Thomas A. “Reminiscences of a Real-Time Researcher.” In <i>Real Time and Such</i>, edited by Susanne Graf, Paul Pettersson, and Bernhard Steffen, 15230:154–64. LNCS. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-73751-0_12\">https://doi.org/10.1007/978-3-031-73751-0_12</a>."},"day":"23","abstract":[{"text":"I give a personal account about the wave of new research activities that rose in the 1990s on the specification, verification, and control of real-time systems.","lang":"eng"}],"_id":"18563","language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_chapter","series_title":"LNCS","article_processing_charge":"No","corr_author":"1","publisher":"Springer Nature","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"volume":15230,"month":"10","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-031-73751-0_12","acknowledgement":"I thank all my collaborators over the years. None of the mentioned contributions would have been possible without them. I also apologize for all omissions. The selection of contributions in this essay reflects primarily my personal involvement rather than any measure of importance.","title":"Reminiscences of a Real-Time Researcher","alternative_title":["LNCS"],"date_created":"2024-11-18T09:10:06Z","OA_type":"closed access","oa_version":"None","place":"Cham","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031737503"],"eisbn":["9783031737510"]},"publication_status":"published"},{"file_date_updated":"2024-12-09T12:54:55Z","date_updated":"2025-09-30T10:40:48Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","ec_funded":1,"abstract":[{"lang":"eng","text":"Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al.  Relevant information can be found in the 'README.txt' files. "}],"_id":"18579","type":"research_data","has_accepted_license":"1","citation":{"ista":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","ama":"Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>","chicago":"Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>.","short":"T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024).","ieee":"T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024.","mla":"Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18579\">10.15479/AT:ISTA:18579</a>.","apa":"Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18579\">https://doi.org/10.15479/AT:ISTA:18579</a>"},"day":"09","year":"2024","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-12-09T00:00:00Z","OA_place":"publisher","acknowledgement":"Freyja Lange, Michael Schunn, and Todor Asenov","doi":"10.15479/AT:ISTA:18579","oa":1,"author":[{"last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","orcid":"0000-0002-4792-1881","last_name":"Sumser","full_name":"Sumser, Anton L"},{"orcid":"0000-0003-2012-9947","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner"},{"full_name":"Schmidt, Florian","last_name":"Schmidt","first_name":"Florian","id":"A2EF226A-AF19-11E9-924C-0525E6697425"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"}],"project":[{"name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus"},{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention"},{"grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses"}],"month":"12","department":[{"_id":"MaJö"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"used_in_publication","id":"19076","status":"public"}]},"file":[{"relation":"main_file","file_id":"18625","creator":"symonova","date_updated":"2024-12-09T10:24:25Z","checksum":"8b13990ca1a458ae3f3ae54c2e888564","file_name":"electro_physiology_data.zip","content_type":"application/x-zip-compressed","date_created":"2024-12-06T13:28:18Z","file_size":800647957,"access_level":"open_access"},{"success":1,"content_type":"application/x-zip-compressed","file_size":828410832,"date_created":"2024-12-09T10:21:10Z","access_level":"open_access","date_updated":"2024-12-09T10:21:10Z","creator":"symonova","relation":"main_file","file_id":"18636","checksum":"c5a4d71c5f29c009c3d96a3244532afa","file_name":"NN_vLGN_Ca_data.zip"},{"file_id":"18637","relation":"main_file","date_updated":"2024-12-09T12:54:55Z","creator":"symonova","checksum":"63651df0186196969553dc48b467f6ab","file_name":"readme.txt","success":1,"content_type":"text/plain","file_size":505,"date_created":"2024-12-09T12:54:55Z","access_level":"open_access"}],"date_created":"2024-11-22T13:48:12Z","title":"A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics","oa_version":"Published Version"},{"publication_status":"published","file":[{"access_level":"open_access","date_created":"2024-12-03T14:10:54Z","file_size":1426555,"success":1,"content_type":"application/pdf","file_name":"2024_NatureComm_Luschnig.pdf","checksum":"3a31af06f52100d287f1e9d9c2aa1d40","date_updated":"2024-12-03T14:10:54Z","file_id":"18615","creator":"dernst","relation":"main_file"}],"publication_identifier":{"eissn":["2041-1723"]},"date_created":"2024-11-24T23:01:48Z","title":"Over 25 years of decrypting PIN-mediated plant development","OA_type":"gold","oa_version":"Published Version","oa":1,"doi":"10.1038/s41467-024-54240-y","acknowledgement":"We gratefully acknowledge Leo Gälweiler for authorizing his PIN1 story. We would like to thank Yuanrong Pei for invaluable help with preparing figures. Work in the lab of C.L. is supported by grants from the Austrian Science Fund (PAT 8419423) and by the Gesellschaft für Forschungsförderung Niederösterreich m.b.H. (FTI19-008). The lab of J.F. is supported by the Austrian Science Fund (I 6123-B and P 37051-B).","author":[{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":15,"department":[{"_id":"JiFr"}],"month":"12","project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"article_type":"original","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","publisher":"Springer Nature","pmid":1,"external_id":{"isi":["001356232600004"],"pmid":["39548100"]},"abstract":[{"text":"Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field.","lang":"eng"}],"_id":"18582","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","day":"01","citation":{"ieee":"C. Luschnig and J. Friml, “Over 25 years of decrypting PIN-mediated plant development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"C. Luschnig, J. Friml, Nature Communications 15 (2024).","mla":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>, vol. 15, 9904, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>.","apa":"Luschnig, C., &#38; Friml, J. (2024). Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>","ista":"Luschnig C, Friml J. 2024. Over 25 years of decrypting PIN-mediated plant development. Nature Communications. 15, 9904.","ama":"Luschnig C, Friml J. Over 25 years of decrypting PIN-mediated plant development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-54240-y\">10.1038/s41467-024-54240-y</a>","chicago":"Luschnig, Christian, and Jiří Friml. “Over 25 Years of Decrypting PIN-Mediated Plant Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-54240-y\">https://doi.org/10.1038/s41467-024-54240-y</a>."},"has_accepted_license":"1","intvolume":"        15","article_number":"9904","ddc":["580"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","OA_place":"publisher","date_published":"2024-12-01T00:00:00Z","file_date_updated":"2024-12-03T14:10:54Z","publication":"Nature Communications","date_updated":"2025-09-08T14:53:48Z","isi":1,"status":"public","DOAJ_listed":"1","scopus_import":"1"},{"pmid":1,"publisher":"Elsevier","article_processing_charge":"Yes (in subscription journal)","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"month":"12","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"article_type":"original","author":[{"first_name":"Michaela","last_name":"Králová","full_name":"Králová, Michaela"},{"last_name":"Kubalová","full_name":"Kubalová, Ivona","first_name":"Ivona"},{"first_name":"Jakub","full_name":"Hajný, Jakub","last_name":"Hajný"},{"orcid":"0000-0001-5630-9419","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","first_name":"Karolina","full_name":"Kubiasova, Karolina","last_name":"Kubiasova"},{"first_name":"Karolína","last_name":"Vagaská","full_name":"Vagaská, Karolína"},{"id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","first_name":"Zengxiang","orcid":"0000-0001-9381-3577","last_name":"Ge","full_name":"Ge, Zengxiang"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana","last_name":"Semerádová","full_name":"Semerádová, Hana"},{"full_name":"Kuchařová, Anna","last_name":"Kuchařová","first_name":"Anna"},{"first_name":"Martin","last_name":"Hönig","full_name":"Hönig, Martin"},{"full_name":"Monzer, Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline"},{"first_name":"Martin","last_name":"Kovačik","full_name":"Kovačik, Martin"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Ikeda","full_name":"Ikeda, Yoshihisa","first_name":"Yoshihisa"},{"full_name":"Zalabák, David","last_name":"Zalabák","first_name":"David"}],"volume":17,"oa":1,"doi":"10.1016/j.molp.2024.11.001","acknowledgement":"We dedicate this paper to the deceased Petr Galuszka for his inspiration and support of our project. We thank Prof. Peter Hedden for constructive criticism of the manuscript and English editing. No conflict of interest is declared.","OA_type":"hybrid","oa_version":"Published Version","title":"A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis","date_created":"2024-11-28T11:13:35Z","publication_identifier":{"issn":["1674-2052"]},"file":[{"checksum":"a11feea4b1677df76b632eca04bfc1dd","file_name":"2024_MolecularPlant_Kralova.pdf","date_updated":"2024-12-03T11:08:09Z","creator":"dernst","file_id":"18612","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","date_created":"2024-12-03T11:08:09Z","file_size":3308945}],"publication_status":"published","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"12","status":"public","page":"1850-1865","isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication":"Molecular Plant","date_updated":"2025-09-08T14:46:45Z","file_date_updated":"2024-12-03T11:08:09Z","OA_place":"publisher","date_published":"2024-12-02T00:00:00Z","ddc":["580"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","intvolume":"        17","day":"02","citation":{"mla":"Králová, Michaela, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>, vol. 17, no. 12, Elsevier, 2024, pp. 1850–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>.","short":"M. Králová, I. Kubalová, J. Hajný, K. Kubiasova, K. Vagaská, Z. Ge, M.C. Gallei, H. Semerádová, A. Kuchařová, M. Hönig, A. Monzer, M. Kovačik, J. Friml, O. Novák, E. Benková, Y. Ikeda, D. Zalabák, Molecular Plant 17 (2024) 1850–1865.","ieee":"M. Králová <i>et al.</i>, “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” <i>Molecular Plant</i>, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024.","apa":"Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>","ama":"Králová M, Kubalová I, Hajný J, et al. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. 2024;17(12):1850-1865. doi:<a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">10.1016/j.molp.2024.11.001</a>","ista":"Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865.","chicago":"Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>."},"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"isi":["001373778300001"],"pmid":["39501563"]},"abstract":[{"text":"Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.","lang":"eng"}],"_id":"18596","language":[{"iso":"eng"}]},{"publication_identifier":{"isbn":["9783031765537"],"issn":["0302-9743"],"eissn":["1611-3349"]},"oa_version":"None","OA_type":"closed access","date_created":"2024-12-01T23:01:52Z","title":"Monitoring extended hypernode logic","alternative_title":["LNCS"],"publication_status":"published","publisher":"Springer Nature","corr_author":"1","article_processing_charge":"No","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, and by the Austrian Science Fund (FWF) SFB project SpyCoDe F8502.","doi":"10.1007/978-3-031-76554-4_9","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"},{"_id":"34a1b658-11ca-11ed-8bc3-c75229f0241e","grant_number":"F8502","name":"Interface Theory for Security and Privacy"}],"month":"11","department":[{"_id":"ToHe"}],"volume":15234,"author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","full_name":"Chalupa, Marek","last_name":"Chalupa"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"full_name":"Oliveira da Costa, Ana","last_name":"Oliveira da Costa","first_name":"Ana","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","orcid":"0000-0002-8741-5799"}],"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"     15234","date_published":"2024-11-13T00:00:00Z","type":"conference","quality_controlled":"1","abstract":[{"lang":"eng","text":"Hypernode logic can reason about the prefix relation on stutter-reduced finite traces through the stutter-reduced prefix predicate. We increase the expressiveness of hypernode logic in two ways. First, we split the stutter-reduced prefix predicate into an explicit stutter-reduction operator and the classical prefix predicate on words. This change gives hypernode logic the ability to combine synchronous and asynchronous reasoning by explicitly stating which parts of traces can stutter. Second, we allow the use of regular expressions in formulas to reason about the structure of traces. This change enables hypernode logic to describe a mixture of trace properties and hyperproperties.\r\n\r\nWe show how to translate extended hypernode logic formulas into multi-track automata, which are automata that read multiple input words. Then we describe a fully online monitoring algorithm for monitoring k-safety hyperproperties specified in the logic. We have implemented the monitoring algorithm, and evaluated it on monitoring synchronous and asynchronous versions of observational determinism, and on checking the privacy preservation by compiler optimizations."}],"_id":"18599","language":[{"iso":"eng"}],"external_id":{"isi":["001416640500009"]},"citation":{"chicago":"Chalupa, Marek, Thomas A Henzinger, and Ana Oliveira da Costa. “Monitoring Extended Hypernode Logic.” In <i>Integrated Formal Methods</i>, 15234:151–71. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-76554-4_9\">https://doi.org/10.1007/978-3-031-76554-4_9</a>.","ama":"Chalupa M, Henzinger TA, Oliveira da Costa A. Monitoring extended hypernode logic. In: <i>Integrated Formal Methods</i>. Vol 15234. Springer Nature; 2024:151-171. doi:<a href=\"https://doi.org/10.1007/978-3-031-76554-4_9\">10.1007/978-3-031-76554-4_9</a>","ista":"Chalupa M, Henzinger TA, Oliveira da Costa A. 2024. Monitoring extended hypernode logic. Integrated Formal Methods. , LNCS, vol. 15234, 151–171.","apa":"Chalupa, M., Henzinger, T. A., &#38; Oliveira da Costa, A. (2024). Monitoring extended hypernode logic. In <i>Integrated Formal Methods</i> (Vol. 15234, pp. 151–171). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-76554-4_9\">https://doi.org/10.1007/978-3-031-76554-4_9</a>","mla":"Chalupa, Marek, et al. “Monitoring Extended Hypernode Logic.” <i>Integrated Formal Methods</i>, vol. 15234, Springer Nature, 2024, pp. 151–71, doi:<a href=\"https://doi.org/10.1007/978-3-031-76554-4_9\">10.1007/978-3-031-76554-4_9</a>.","short":"M. Chalupa, T.A. Henzinger, A. Oliveira da Costa, in:, Integrated Formal Methods, Springer Nature, 2024, pp. 151–171.","ieee":"M. Chalupa, T. A. Henzinger, and A. Oliveira da Costa, “Monitoring extended hypernode logic,” in <i>Integrated Formal Methods</i>, 2024, vol. 15234, pp. 151–171."},"day":"13","status":"public","page":"151-171","scopus_import":"1","ec_funded":1,"isi":1,"date_updated":"2025-09-08T14:47:22Z","publication":"Integrated Formal Methods"}]