[{"volume":37,"date_updated":"2025-05-14T11:34:20Z","ddc":["000"],"publication_identifier":{"eissn":["1049-5258"]},"publisher":"Neural Information Processing Systems Foundation","alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Published Version","publication":"38th Annual Conference on Neural Information Processing Systems","OA_type":"gold","external_id":{"arxiv":["2405.13763"]},"publication_status":"published","arxiv":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","language":[{"iso":"eng"}],"citation":{"ama":"Kalinin N, Lampert C. Banded square root matrix factorization for differentially private model training. In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","chicago":"Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","apa":"Kalinin, N., &#38; Lampert, C. (2024). Banded square root matrix factorization for differentially private model training. In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"N. Kalinin and C. Lampert, “Banded square root matrix factorization for differentially private model training,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","mla":"Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","short":"N. Kalinin, C. Lampert, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ista":"Kalinin N, Lampert C. 2024. Banded square root matrix factorization for differentially private model training. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37."},"date_created":"2025-01-24T17:58:16Z","title":"Banded square root matrix factorization for differentially private model training","status":"public","_id":"18875","abstract":[{"lang":"eng","text":"Current state-of-the-art methods for differentially private model training are based on matrix factorization techniques. However, these methods suffer from high computational overhead because they require numerically solving a demanding optimization problem to determine an approximately optimal factorization prior to the actual model training. In this work, we present a new matrix factorization approach, BSR, which overcomes this computational bottleneck. By exploiting properties of the standard matrix square root, BSR allows to efficiently handle also large-scale problems. For the key scenario of stochastic gradient descent with momentum and weight decay, we even derive analytical expressions for BSR that render the computational overhead negligible. We prove bounds on the approximation quality that hold both in the centralized and in the federated learning setting. Our numerical experiments demonstrate that models trained using BSR perform on par with the best existing methods, while completely avoiding their computational overhead."}],"scopus_import":"1","conference":{"start_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","end_date":"2024-12-16"},"has_accepted_license":"1","oa":1,"date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","file":[{"file_name":"2024_NeurIPS_Nikita.pdf","success":1,"relation":"main_file","date_created":"2025-01-27T09:52:15Z","content_type":"application/pdf","file_id":"18888","creator":"dernst","checksum":"a216cab8eddc1fe7840aede0e2c0d41e","date_updated":"2025-01-27T09:52:15Z","file_size":1144656,"access_level":"open_access"}],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"corr_author":"1","intvolume":"        37","year":"2024","article_processing_charge":"No","file_date_updated":"2025-01-27T09:52:15Z","OA_place":"publisher","author":[{"first_name":"Nikita","last_name":"Kalinin","id":"4b14526e-14d2-11ed-ba64-c14c9553d137","full_name":"Kalinin, Nikita"},{"first_name":"Christoph","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12"},{"citation":{"ama":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. Average gradient outer product as a mechanism for deep neural collapse. In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","chicago":"Beaglehole, Daniel, Peter Súkeník, Marco Mondelli, and Mikhail Belkin. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","apa":"Beaglehole, D., Súkeník, P., Mondelli, M., &#38; Belkin, M. (2024). Average gradient outer product as a mechanism for deep neural collapse. In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"D. Beaglehole, P. Súkeník, M. Mondelli, and M. Belkin, “Average gradient outer product as a mechanism for deep neural collapse,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","mla":"Beaglehole, Daniel, et al. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","short":"D. Beaglehole, P. Súkeník, M. Mondelli, M. Belkin, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ista":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. 2024. Average gradient outer product as a mechanism for deep neural collapse. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37."},"language":[{"iso":"eng"}],"date_created":"2025-01-27T11:11:40Z","main_file_link":[{"url":"https://openreview.net/forum?id=lJ1jdl2K9k","open_access":"1"}],"oa_version":"Preprint","OA_type":"green","publication":"38th Annual Conference on Neural Information Processing Systems","type":"conference","publication_status":"published","external_id":{"arxiv":["2402.13728"]},"arxiv":1,"alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems Foundation","publication_identifier":{"eissn":["1049-5258"]},"acknowledgement":"We acknowledge support from the National Science Foundation (NSF) and the Simons Foundation for the Collaboration on the Theoretical Foundations of Deep Learning through awards DMS-2031883 and #814639 as well as the TILOS institute (NSF CCF-2112665). This work used the programs (1) XSEDE (Extreme science and engineering discovery environment) which is supported by NSF grant numbers ACI-1548562, and (2) ACCESS (Advanced cyberinfrastructure coordination ecosystem: services & support) which is supported by NSF grants numbers #2138259, #2138286, #2138307, #2137603, and #2138296. Specifically, we used the resources from SDSC Expanse GPU compute nodes, and NCSA Delta system, via allocations TG-CIS220009. Marco Mondelli is supported by the 2019 Lopez-Loreta prize. We also acknowledge useful feedback from anonymous reviewers. ","volume":37,"date_updated":"2025-05-14T11:29:45Z","OA_place":"repository","article_processing_charge":"No","month":"12","author":[{"full_name":"Beaglehole, Daniel","last_name":"Beaglehole","first_name":"Daniel"},{"first_name":"Peter","full_name":"Súkeník, Peter","last_name":"Súkeník","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"first_name":"Mikhail","full_name":"Belkin, Mikhail","last_name":"Belkin"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        37","year":"2024","oa":1,"department":[{"_id":"GradSch"},{"_id":"MaMo"}],"corr_author":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","date_published":"2024-12-01T00:00:00Z","title":"Average gradient outer product as a mechanism for deep neural collapse","conference":{"end_date":"2024-12-16","location":"Vancouver, Canada","start_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems"},"scopus_import":"1","_id":"18890","abstract":[{"text":"Deep Neural Collapse (DNC) refers to the surprisingly rigid structure of the data representations in the final layers of Deep Neural Networks (DNNs). Though the phenomenon has been measured in a variety of settings, its emergence is typically explained via data-agnostic approaches, such as the unconstrained features model. In this work, we introduce a data-dependent setting where DNC forms due to feature learning through the average gradient outer product (AGOP). The AGOP is defined with respect to a learned predictor and is equal to the uncentered covariance matrix of its input-output gradients averaged over the training dataset. The Deep Recursive Feature Machine (Deep RFM) is a method that constructs a neural network by iteratively mapping the data with the AGOP and applying an untrained random feature map. We demonstrate empirically that DNC occurs in Deep RFM across standard settings as a consequence of the projection with the AGOP matrix computed at each layer. Further, we theoretically explain DNC in Deep RFM in an asymptotic setting and as a result of kernel learning. We then provide evidence that this mechanism holds for neural networks more generally. In particular, we show that the right singular vectors and values of the weights can be responsible for the majority of within-class variability collapse for DNNs trained in the feature learning regime. As observed in recent work, this singular structure is highly correlated with that of the AGOP.","lang":"eng"}],"status":"public"},{"alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems Foundation","ddc":["000"],"date_updated":"2025-06-04T07:19:21Z","volume":37,"acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","date_created":"2025-01-27T11:15:18Z","language":[{"iso":"eng"}],"citation":{"chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024."},"external_id":{"arxiv":["2405.14468"]},"publication_status":"published","arxiv":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","oa_version":"Published Version","OA_type":"gold","publication":"38th Annual Conference on Neural Information Processing Systems","date_published":"2024-12-01T00:00:00Z","file":[{"file_id":"18989","creator":"dernst","content_type":"application/pdf","date_updated":"2025-02-04T08:11:25Z","file_size":1784118,"access_level":"open_access","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","file_name":"2024_NeurIPS_Sukenik.pdf","success":1,"relation":"main_file","date_created":"2025-02-04T08:11:25Z"}],"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"corr_author":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"has_accepted_license":"1","oa":1,"_id":"18891","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent."}],"status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16","location":"Vancouver, Canada","end_date":"2024-12-16"},"title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","day":"01","author":[{"id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník","full_name":"Súkeník, Peter","first_name":"Peter"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","article_processing_charge":"No","file_date_updated":"2025-02-04T08:11:25Z","OA_place":"publisher","year":"2024","acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":"        37"},{"day":"23","author":[{"first_name":"Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","last_name":"Cadei","full_name":"Cadei, Riccardo"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868"},{"first_name":"Lukas","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","last_name":"Lindorfer","full_name":"Lindorfer, Lukas"},{"first_name":"Cordelia","full_name":"Schmid, Cordelia","last_name":"Schmid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-27T11:45:43Z","month":"10","article_processing_charge":"No","citation":{"mla":"Cadei, Riccardo, et al. <i>ISTAnt</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","short":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024).","ista":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ama":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>","chicago":"Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>.","apa":"Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., &#38; Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>","ieee":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024."},"fulldoi":"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2","OA_place":"repository","year":"2024","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://10.6084/M9.FIGSHARE.26484934.V2"}],"oa_version":"Published Version","OA_type":"gold","date_published":"2024-10-23T00:00:00Z","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["570"],"_id":"18895","abstract":[{"text":"ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \\citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file).","lang":"eng"}],"status":"public","related_material":{"record":[{"id":"18847","status":"public","relation":"used_in_publication"}]},"date_updated":"2025-01-27T11:58:38Z","doi":"10.6084/M9.FIGSHARE.26484934.V2","title":"ISTAnt"},{"year":"2024","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","full_name":"Pedrotti, Francesco"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco"}],"day":"01","OA_place":"publisher","file_date_updated":"2025-01-27T12:19:44Z","article_processing_charge":"No","scopus_import":"1","status":"public","_id":"18897","abstract":[{"lang":"eng","text":"Score-based generative models (SGMs) are powerful tools to sample from complex data distributions. Their underlying idea is to (i) run a forward process for time T1 by adding noise to the data, (ii) estimate its score function, and (iii) use such estimate to run a reverse process. As the reverse process is initialized with the stationary distribution of the forward one, the existing analysis paradigm requires T1→∞. This is however problematic: from a theoretical viewpoint, for a given precision of the score approximation, the convergence guarantee fails as T1 diverges; from a practical viewpoint, a large T1 increases computational costs and leads to error propagation. This paper addresses the issue by considering a version of the popular predictor-corrector scheme: after running the forward process, we first estimate the final distribution via an inexact Langevin dynamics and then revert the process. Our key technical contribution is to provide convergence guarantees which require to run the forward process only for a fixed finite time T1. Our bounds exhibit a mild logarithmic dependence on the input dimension and the subgaussian norm of the target distribution, have minimal assumptions on the data, and require only to control the L2 loss on the score approximation, which is the quantity minimized in practice."}],"title":"Improved convergence of score-based diffusion models via prediction-correction","corr_author":"1","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"department":[{"_id":"JaMa"},{"_id":"MaMo"}],"date_published":"2024-06-01T00:00:00Z","quality_controlled":"1","file":[{"content_type":"application/pdf","file_id":"18898","creator":"dernst","checksum":"76a1fd5afd8ee6f7ae0e5912d7dbf6b4","date_updated":"2025-01-27T12:19:44Z","access_level":"open_access","file_size":780315,"success":1,"file_name":"2024_TMLR_Pedrotti.pdf","date_created":"2025-01-27T12:19:44Z","relation":"main_file"}],"oa":1,"has_accepted_license":"1","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"arxiv":1,"external_id":{"arxiv":["2305.14164"]},"publication_status":"published","publication":"Transactions on Machine Learning Research","OA_type":"gold","oa_version":"Published Version","date_created":"2025-01-27T12:18:05Z","citation":{"mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <i>Transactions on Machine Learning Research</i>, 2024.","short":"F. Pedrotti, J. Maas, M. Mondelli, in:, Transactions on Machine Learning Research, 2024.","ista":"Pedrotti F, Maas J, Mondelli M. 2024. Improved convergence of score-based diffusion models via prediction-correction. Transactions on Machine Learning Research. , TMLR, .","ama":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. In: <i>Transactions on Machine Learning Research</i>. ; 2024.","chicago":"Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” In <i>Transactions on Machine Learning Research</i>, 2024.","apa":"Pedrotti, F., Maas, J., &#38; Mondelli, M. (2024). Improved convergence of score-based diffusion models via prediction-correction. In <i>Transactions on Machine Learning Research</i>.","ieee":"F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” in <i>Transactions on Machine Learning Research</i>, 2024."},"language":[{"iso":"eng"}],"date_updated":"2025-04-15T08:31:35Z","related_material":{"record":[{"id":"17350","status":"public","relation":"earlier_version"}]},"acknowledgement":"Francesco Pedrotti and Jan Maas acknowledge support by the Austrian Science Fund (FWF) project 10.55776/F65. Marco Mondelli acknowledges support by the 2019 Lopez-Loreta prize.\r\n","alternative_title":["TMLR"],"publication_identifier":{"issn":["2835-8856"]},"ddc":["000"]},{"date_created":"2025-01-27T12:26:03Z","place":"Cham","citation":{"ieee":"J. Maas, S. A. E. Rademacher, T. Titkos, and D. Virosztek, Eds., <i>Optimal Transport on Quantum Structures</i>, vol. 29. Cham: Springer Nature, 2024.","apa":"Maas, J., Rademacher, S. A. E., Titkos, T., &#38; Virosztek, D. (Eds.). (2024). <i>Optimal Transport on Quantum Structures</i> (Vol. 29). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>","chicago":"Maas, Jan, Simone Anna Elvira Rademacher, Tamás Titkos, and Daniel Virosztek, eds. <i>Optimal Transport on Quantum Structures</i>. Vol. 29. BSMS. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>.","ama":"Maas J, Rademacher SAE, Titkos T, Virosztek D, eds. <i>Optimal Transport on Quantum Structures</i>. Vol 29. Cham: Springer Nature; 2024. doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>","ista":"Maas J, Rademacher SAE, Titkos T, Virosztek D eds. 2024. Optimal Transport on Quantum Structures, Cham: Springer Nature,p.","short":"J. Maas, S.A.E. Rademacher, T. Titkos, D. Virosztek, eds., Optimal Transport on Quantum Structures, Springer Nature, Cham, 2024.","mla":"Maas, Jan, et al., editors. <i>Optimal Transport on Quantum Structures</i>. Vol. 29, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>."},"language":[{"iso":"eng"}],"type":"book_editor","publication_status":"published","oa_version":"None","publisher":"Springer Nature","alternative_title":["Bolyai Society Mathematical Studies"],"editor":[{"orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"},{"full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466"},{"last_name":"Titkos","full_name":"Titkos, Tamás","first_name":"Tamás"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel","first_name":"Daniel","orcid":"0000-0003-1109-5511"}],"publication_identifier":{"eissn":["2947-9460"],"issn":["1217-4696"],"isbn":["9783031504655"],"eisbn":["9783031504662"]},"date_updated":"2025-02-17T12:22:18Z","volume":29,"month":"09","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-3-031-50466-2","article_processing_charge":"No","year":"2024","intvolume":"        29","department":[{"_id":"JaMa"}],"date_published":"2024-09-19T00:00:00Z","quality_controlled":"1","scopus_import":"1","series_title":"BSMS","_id":"18899","status":"public","abstract":[{"lang":"eng","text":"The flourishing theory of classical optimal transport concerns mass transportation at minimal cost. This book introduces the reader to optimal transport on quantum structures, i.e., optimal transportation between quantum states and related non-commutative concepts of mass transportation. It contains lecture notes on\r\n\r\nclassical optimal transport and Wasserstein gradient flows\r\ndynamics and quantum optimal transport\r\nquantum couplings and many-body problems\r\nquantum channels and qubits\r\n\r\nThese notes are based on lectures given by the authors at the \"Optimal Transport on Quantum Structures\" School held at the Erdös Center in Budapest in the fall of 2022. The lecture notes are complemented by two survey chapters presenting the state of the art in different research areas of non-commutative optimal transport."}],"title":"Optimal Transport on Quantum Structures","doi":"10.1007/978-3-031-50466-2"},{"year":"2024","intvolume":"      2024","issue":"14","month":"07","author":[{"orcid":"0000-0002-0519-4241","first_name":"Melchior","full_name":"Wirth, Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"day":"01","page":"10597-10614","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"OA_place":"publisher","fulldoi":"https://doi.org/10.1093/imrn/rnae092","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2025-01-27T12:38:10Z","article_type":"original","scopus_import":"1","_id":"18900","status":"public","abstract":[{"lang":"eng","text":"We prove that certain closable derivations on the GNS Hilbert space associated with a non-tracial weight on a von Neumann algebra give rise to GNS-symmetric semigroups of contractive completely positive maps on the von Neumann algebra."}],"title":"Modular completely Dirichlet forms as squares of derivations","doi":"10.1093/imrn/rnae092","department":[{"_id":"JaMa"}],"corr_author":"1","project":[{"name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","grant_number":"ESP156_N"}],"date_published":"2024-07-01T00:00:00Z","file":[{"relation":"main_file","date_created":"2025-01-27T12:38:10Z","file_name":"2024_IMRN_Wirth.pdf","success":1,"access_level":"open_access","file_size":689984,"date_updated":"2025-01-27T12:38:10Z","checksum":"3e1f80d58ada0c60a58f35df8080967e","creator":"dernst","file_id":"18901","content_type":"application/pdf"}],"quality_controlled":"1","oa":1,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","publication_status":"published","external_id":{"isi":["001222279400001"]},"oa_version":"Published Version","OA_type":"hybrid","publication":"International Mathematics Research Notices","date_created":"2025-01-27T12:36:10Z","citation":{"ama":"Wirth M. Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. 2024;2024(14):10597-10614. doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>","chicago":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>.","apa":"Wirth, M. (2024). Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>","ieee":"M. Wirth, “Modular completely Dirichlet forms as squares of derivations,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14. Oxford University Press, pp. 10597–10614, 2024.","mla":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14, Oxford University Press, 2024, pp. 10597–614, doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>.","short":"M. Wirth, International Mathematics Research Notices 2024 (2024) 10597–10614.","ista":"Wirth M. 2024. Modular completely Dirichlet forms as squares of derivations. International Mathematics Research Notices. 2024(14), 10597–10614."},"language":[{"iso":"eng"}],"date_updated":"2025-09-09T12:02:46Z","acknowledgement":"The author was funded by the Austrian Science Fund under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. ","volume":2024,"publisher":"Oxford University Press","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"ddc":["510"]},{"intvolume":"        15","year":"2024","article_processing_charge":"Yes","file_date_updated":"2025-01-27T13:04:03Z","isi":1,"OA_place":"publisher","fulldoi":"https://doi.org/10.1038/s41467-024-45148-8","author":[{"last_name":"Zagorski","full_name":"Zagorski, Marcin","first_name":"Marcin"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"first_name":"Matthias","last_name":"Lutolf","full_name":"Lutolf, Matthias"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"02","doi":"10.1038/s41467-024-45148-8","title":"Assessing the precision of morphogen gradients in neural tube development","pmid":1,"_id":"18902","status":"public","scopus_import":"1","article_type":"letter_note","has_accepted_license":"1","oa":1,"date_published":"2024-02-01T00:00:00Z","quality_controlled":"1","file":[{"relation":"main_file","date_created":"2025-01-27T13:04:03Z","file_name":"2024_NatureComm_Zagorski.pdf","success":1,"checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7","file_size":4723831,"access_level":"open_access","date_updated":"2025-01-27T13:04:03Z","content_type":"application/pdf","creator":"dernst","file_id":"18903"}],"department":[{"_id":"GaTk"},{"_id":"AnKi"}],"project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"corr_author":"1","oa_version":"Published Version","publication":"Nature Communications","OA_type":"gold","external_id":{"isi":["001156218500022"],"pmid":["38302459"]},"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"article_number":"929","citation":{"ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929.","short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>.","ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>","chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>"},"date_created":"2025-01-27T13:01:01Z","volume":15,"acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","date_updated":"2025-12-30T10:57:08Z","DOAJ_listed":"1","ddc":["570"],"publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature"},{"OA_place":"publisher","fulldoi":"https://doi.org/10.1145/3637528.3671978","isi":1,"file_date_updated":"2025-01-27T13:25:23Z","article_processing_charge":"Yes (in subscription journal)","month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Kathrin","full_name":"Hanauer, Kathrin","last_name":"Hanauer"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Robin","full_name":"Münk, Robin","last_name":"Münk"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"last_name":"Vötsch","full_name":"Vötsch, Maximilian","first_name":"Maximilian"}],"day":"01","page":"1016-1027","year":"2024","ec_funded":1,"oa":1,"has_accepted_license":"1","project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"}],"department":[{"_id":"MoHe"}],"file":[{"content_type":"application/pdf","file_id":"18907","creator":"dernst","checksum":"1265d5cf6aa5f94157631651723c4a2b","date_updated":"2025-01-27T13:25:23Z","access_level":"open_access","file_size":1450331,"success":1,"file_name":"2024_ACMKDD_Hanauer.pdf","date_created":"2025-01-27T13:25:23Z","relation":"main_file"}],"date_published":"2024-09-01T00:00:00Z","quality_controlled":"1","title":"Expander hierarchies for normalized cuts on graphs","doi":"10.1145/3637528.3671978","conference":{"start_date":"2024-08-05","name":"KDD: Knowledge Discovery and Data Mining","location":"Barcelona, Spain","end_date":"2024-08-29"},"scopus_import":"1","_id":"18906","abstract":[{"lang":"eng","text":"Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective.\r\nOur extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time."}],"status":"public","citation":{"ama":"Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. Expander hierarchies for normalized cuts on graphs. In: <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>. ACM; 2024:1016-1027. doi:<a href=\"https://doi.org/10.1145/3637528.3671978\">10.1145/3637528.3671978</a>","chicago":"Hanauer, Kathrin, Monika Henzinger, Robin Münk, Harald Räcke, and Maximilian Vötsch. “Expander Hierarchies for Normalized Cuts on Graphs.” In <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, 1016–27. ACM, 2024. <a href=\"https://doi.org/10.1145/3637528.3671978\">https://doi.org/10.1145/3637528.3671978</a>.","apa":"Hanauer, K., Henzinger, M., Münk, R., Räcke, H., &#38; Vötsch, M. (2024). Expander hierarchies for normalized cuts on graphs. In <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i> (pp. 1016–1027). Barcelona, Spain: ACM. <a href=\"https://doi.org/10.1145/3637528.3671978\">https://doi.org/10.1145/3637528.3671978</a>","ieee":"K. Hanauer, M. Henzinger, R. Münk, H. Räcke, and M. Vötsch, “Expander hierarchies for normalized cuts on graphs,” in <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, Barcelona, Spain, 2024, pp. 1016–1027.","mla":"Hanauer, Kathrin, et al. “Expander Hierarchies for Normalized Cuts on Graphs.” <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, ACM, 2024, pp. 1016–27, doi:<a href=\"https://doi.org/10.1145/3637528.3671978\">10.1145/3637528.3671978</a>.","short":"K. Hanauer, M. Henzinger, R. Münk, H. Räcke, M. Vötsch, in:, Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, ACM, 2024, pp. 1016–1027.","ista":"Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. 2024. Expander hierarchies for normalized cuts on graphs. Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. KDD: Knowledge Discovery and Data Mining, 1016–1027."},"language":[{"iso":"eng"}],"date_created":"2025-01-27T13:20:26Z","publication":"Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining","OA_type":"hybrid","oa_version":"Published Version","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["001324524201013"]},"publication_status":"published","ddc":["000"],"publisher":"ACM","publication_identifier":{"isbn":["9798400704901"]},"acknowledgement":"Monika Henzinger: This project has received funding from the European Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke, Robin Münk: This project has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 498605858 and 470029389.","date_updated":"2025-09-09T12:04:56Z"},{"date_published":"2024-07-01T00:00:00Z","quality_controlled":"1","corr_author":"1","department":[{"_id":"BeBi"}],"doi":"10.1145/3641519.3657453","title":"Fabricable 3D wire art","_id":"18912","abstract":[{"text":"This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.","lang":"eng"}],"status":"public","conference":{"end_date":"2024-08-01","location":"Denver, CO, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28"},"scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1145/3641519.3657453","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","author":[{"full_name":"Tojo, Kenji","last_name":"Tojo","first_name":"Kenji"},{"last_name":"Shamir","full_name":"Shamir, Ariel","first_name":"Ariel"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"}],"month":"07","year":"2024","publication_identifier":{"isbn":["9798400705250"]},"publisher":"ACM","acknowledgement":"The authors thank the anonymous reviewers for their valuable comments and suggestions for improving the paper. This work was supported by JSPS KAKENHI Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan. This work was partially supported by Israel Science Foundation Grant number 1390/19 and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful advice on wire selection and Takeo Igarashi for his assistance in arranging the collaboration of the authors.","date_updated":"2025-09-09T12:06:57Z","language":[{"iso":"eng"}],"citation":{"mla":"Tojo, Kenji, et al. “Fabricable 3D Wire Art.” <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, 134, ACM, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>.","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 134.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, ACM, 2024.","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable 3D Wire Art.” In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM, 2024. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>.","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,” in <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, Denver, CO, United States, 2024.","apa":"Tojo, K., Shamir, A., Bickel, B., &#38; Umetani, N. (2024). Fabricable 3D wire art. In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. Denver, CO, United States: ACM. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>"},"article_number":"134","date_created":"2025-01-27T13:47:35Z","publication":"SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers","OA_type":"closed access","oa_version":"None","external_id":{"isi":["001282218200059"]},"publication_status":"published","type":"conference"},{"conference":{"start_date":"2024-07-01","name":"ASIACCS: Asia Conference on Computer and Communications Security","location":"Singapore, Singapore","end_date":"2024-07-05"},"scopus_import":"1","_id":"18913","abstract":[{"text":"With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.\r\nBy implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols.","lang":"eng"}],"status":"public","title":"An empirical study of consensus protocols’ DoS resilience","doi":"10.1145/3634737.3656997","department":[{"_id":"ElKo"}],"date_published":"2024-07-01T00:00:00Z","file":[{"success":1,"file_name":"2024_ACMAsiaCCS_Giuliari.pdf","relation":"main_file","date_created":"2025-01-27T14:04:12Z","file_id":"18914","creator":"dernst","content_type":"application/pdf","date_updated":"2025-01-27T14:04:12Z","access_level":"open_access","file_size":951940,"checksum":"1e743ddf49d35390eb56e11eb0759150"}],"quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2024","month":"07","page":"1345-1360","day":"01","author":[{"first_name":"Giacomo","last_name":"Giuliari","full_name":"Giuliari, Giacomo"},{"full_name":"Sonnino, Alberto","last_name":"Sonnino","first_name":"Alberto"},{"first_name":"Marc","last_name":"Frei","full_name":"Frei, Marc"},{"full_name":"Streun, Fabio","last_name":"Streun","first_name":"Fabio"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Perrig, Adrian","last_name":"Perrig","first_name":"Adrian"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"OA_place":"publisher","fulldoi":"https://doi.org/10.1145/3634737.3656997","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2025-01-27T14:04:12Z","date_updated":"2025-09-09T12:07:28Z","acknowledgement":"This work was mostly realized while Alberto Sonnino and Lefteris Kokoris-Kogias were employed at Meta. We gratefully acknowledge support for this project from ETH Zurich and Mysten Labs.","publisher":"ACM","publication_identifier":{"isbn":["9798400704826"]},"ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","publication_status":"published","external_id":{"isi":["001283918100095"]},"oa_version":"Published Version","OA_type":"hybrid","publication":"Proceedings of the 19th ACM Asia Conference on Computer and Communications Security","date_created":"2025-01-27T13:57:00Z","citation":{"short":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, A. Perrig, in:, Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–1360.","ista":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. 2024. An empirical study of consensus protocols’ DoS resilience. Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ASIACCS: Asia Conference on Computer and Communications Security, 1345–1360.","mla":"Giuliari, Giacomo, et al. “An Empirical Study of Consensus Protocols’ DoS Resilience.” <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, ACM, 2024, pp. 1345–60, doi:<a href=\"https://doi.org/10.1145/3634737.3656997\">10.1145/3634737.3656997</a>.","apa":"Giuliari, G., Sonnino, A., Frei, M., Streun, F., Kokoris Kogias, E., &#38; Perrig, A. (2024). An empirical study of consensus protocols’ DoS resilience. In <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i> (pp. 1345–1360). Singapore, Singapore: ACM. <a href=\"https://doi.org/10.1145/3634737.3656997\">https://doi.org/10.1145/3634737.3656997</a>","ieee":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, and A. Perrig, “An empirical study of consensus protocols’ DoS resilience,” in <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, Singapore, Singapore, 2024, pp. 1345–1360.","ama":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. An empirical study of consensus protocols’ DoS resilience. In: <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>. ACM; 2024:1345-1360. doi:<a href=\"https://doi.org/10.1145/3634737.3656997\">10.1145/3634737.3656997</a>","chicago":"Giuliari, Giacomo, Alberto Sonnino, Marc Frei, Fabio Streun, Eleftherios Kokoris Kogias, and Adrian Perrig. “An Empirical Study of Consensus Protocols’ DoS Resilience.” In <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, 1345–60. ACM, 2024. <a href=\"https://doi.org/10.1145/3634737.3656997\">https://doi.org/10.1145/3634737.3656997</a>."},"language":[{"iso":"eng"}]},{"title":"Through the slopes of a light-induced phase transition","doi":"10.1038/s41567-024-02401-7","scopus_import":"1","article_type":"letter_note","_id":"18919","status":"public","abstract":[{"lang":"eng","text":"The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling."}],"corr_author":"1","department":[{"_id":"DeBa"}],"date_published":"2024-05-01T00:00:00Z","quality_controlled":"1","intvolume":"        20","year":"2024","fulldoi":"https://doi.org/10.1038/s41567-024-02401-7","isi":1,"article_processing_charge":"No","month":"05","issue":"5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"}],"day":"01","page":"684-685","volume":20,"date_updated":"2025-09-09T12:08:10Z","publisher":"Springer Nature","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication":"Nature Physics","OA_type":"closed access","oa_version":"None","type":"journal_article","publication_status":"published","external_id":{"isi":["001162208200002"]},"citation":{"apa":"Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>","ieee":"D. R. Baykusheva, “Through the slopes of a light-induced phase transition,” <i>Nature Physics</i>, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.","ama":"Baykusheva DR. Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. 2024;20(5):684-685. doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>","chicago":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>.","short":"D.R. Baykusheva, Nature Physics 20 (2024) 684–685.","ista":"Baykusheva DR. 2024. Through the slopes of a light-induced phase transition. Nature Physics. 20(5), 684–685.","mla":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>, vol. 20, no. 5, Springer Nature, 2024, pp. 684–85, doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>."},"language":[{"iso":"eng"}],"date_created":"2025-01-27T14:29:20Z"},{"intvolume":"        10","year":"2024","file_date_updated":"2025-01-27T14:40:08Z","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.1126/sciadv.adk1954","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Homola","full_name":"Homola, Miroslav","first_name":"Miroslav"},{"full_name":"Büttner, Renate Carina","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","last_name":"Büttner","first_name":"Renate Carina"},{"full_name":"Füzik, Tibor","last_name":"Füzik","first_name":"Tibor"},{"full_name":"Křepelka, Pavel","last_name":"Křepelka","first_name":"Pavel"},{"full_name":"Holbová, Radka","last_name":"Holbová","first_name":"Radka"},{"last_name":"Nováček","full_name":"Nováček, Jiří","first_name":"Jiří"},{"first_name":"Marten L.","last_name":"Chaillet","full_name":"Chaillet, Marten L."},{"first_name":"Jakub","last_name":"Žák","full_name":"Žák, Jakub"},{"last_name":"Grybchuk","full_name":"Grybchuk, Danyil","first_name":"Danyil"},{"last_name":"Förster","full_name":"Förster, Friedrich","first_name":"Friedrich"},{"first_name":"William H.","full_name":"Wilson, William H.","last_name":"Wilson"},{"full_name":"Schroeder, Declan C.","last_name":"Schroeder","first_name":"Declan C."},{"last_name":"Plevka","full_name":"Plevka, Pavel","first_name":"Pavel"}],"day":"01","month":"04","issue":"15","doi":"10.1126/sciadv.adk1954","pmid":1,"title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","status":"public","_id":"18920","abstract":[{"lang":"eng","text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis."}],"scopus_import":"1","article_type":"original","has_accepted_license":"1","oa":1,"date_published":"2024-04-01T00:00:00Z","quality_controlled":"1","file":[{"checksum":"291dd7ceccbe6bfd8e0a9157584f88e9","access_level":"open_access","file_size":40623405,"date_updated":"2025-01-27T14:40:08Z","content_type":"application/pdf","creator":"dernst","file_id":"18921","date_created":"2025-01-27T14:40:08Z","relation":"main_file","file_name":"2024_ScienceAdv_Homola.pdf","success":1}],"department":[{"_id":"EM-Fac"}],"publication":"Science Advances","OA_type":"gold","oa_version":"Published Version","external_id":{"pmid":["38598627"]},"publication_status":"published","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"citation":{"chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>.","ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. 2024;10(15). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>","ieee":"M. Homola <i>et al.</i>, “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” <i>Science Advances</i>, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>","mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>.","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024)."},"article_number":"eadk1954 ","date_created":"2025-01-27T14:32:34Z","volume":10,"acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","date_updated":"2025-05-14T09:29:04Z","related_material":{"link":[{"relation":"software","url":" https://github.com/fuzikt/tomostarpy."}]},"DOAJ_listed":"1","ddc":["570"],"publication_identifier":{"eissn":["2375-2548"]},"publisher":"American Association for the Advancement of Science"},{"language":[{"iso":"eng"}],"citation":{"ama":"Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components of directed graphs in linear time. In: <i>65th Annual Symposium on Foundations of Computer Science</i>. IEEE; 2024:62-85. doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>","chicago":"Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In <i>65th Annual Symposium on Foundations of Computer Science</i>, 62–85. IEEE, 2024. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>.","apa":"Georgiadis, L., Italiano, G. F., &#38; Kosinas, E. (2024). Computing the 3-edge-connected components of directed graphs in linear time. In <i>65th Annual Symposium on Foundations of Computer Science</i> (pp. 62–85). Chicago, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>","ieee":"L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected components of directed graphs in linear time,” in <i>65th Annual Symposium on Foundations of Computer Science</i>, Chicago, IL, United States, 2024, pp. 62–85.","mla":"Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” <i>65th Annual Symposium on Foundations of Computer Science</i>, IEEE, 2024, pp. 62–85, doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>.","short":"L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations of Computer Science, IEEE, 2024, pp. 62–85.","ista":"Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected components of directed graphs in linear time. 65th Annual Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science, 62–85."},"date_created":"2025-01-27T14:50:23Z","oa_version":"None","OA_type":"closed access","publication":"65th Annual Symposium on Foundations of Computer Science","external_id":{"isi":["001419526400005"]},"publication_status":"published","type":"conference","publication_identifier":{"isbn":["9798331516741"]},"publisher":"IEEE","acknowledgement":"Giuseppe F. Italiano was partially supported by the Italian Ministry of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n","date_updated":"2025-09-09T12:08:47Z","article_processing_charge":"No","isi":1,"fulldoi":"https://doi.org/10.1109/focs61266.2024.00015","day":"01","author":[{"first_name":"Loukas","last_name":"Georgiadis","full_name":"Georgiadis, Loukas"},{"last_name":"Italiano","full_name":"Italiano, Giuseppe F.","first_name":"Giuseppe F."},{"first_name":"Evangelos","id":"4c7f9625-dbbc-11ee-9d86-bdcc2db5a949","last_name":"Kosinas","full_name":"Kosinas, Evangelos"}],"page":"62-85","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","year":"2024","quality_controlled":"1","date_published":"2024-10-01T00:00:00Z","department":[{"_id":"MoHe"}],"corr_author":"1","doi":"10.1109/focs61266.2024.00015","title":"Computing the 3-edge-connected components of directed graphs in linear time","status":"public","_id":"18922","abstract":[{"lang":"eng","text":"Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them."}],"scopus_import":"1","conference":{"location":"Chicago, IL, United States","name":"FOCS: Foundations of Computer Science","start_date":"2024-10-27","end_date":"2024-10-30"}},{"title":"Congestion-free rerouting of network flows: Hardness and an FPT algorithm","doi":"10.1109/noms59830.2024.10575579","conference":{"location":"Seoul, Republic of Korea","start_date":"2024-05-06","name":"NOMS: Network Operations and Management Symposiu ","end_date":"2024-05-10"},"scopus_import":"1","abstract":[{"lang":"eng","text":"Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature."}],"_id":"18925","status":"public","oa":1,"department":[{"_id":"KrCh"}],"corr_author":"1","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"894907","name":"Graphical Games","_id":"bd622a5c-d553-11ed-ba76-bae280ba8aff"}],"date_published":"2024-05-01T00:00:00Z","quality_controlled":"1","ec_funded":1,"year":"2024","isi":1,"fulldoi":"https://doi.org/10.1109/noms59830.2024.10575579","OA_place":"other","article_processing_charge":"No","month":"05","author":[{"full_name":"Ceylan, Esra","id":"cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933","last_name":"Ceylan","first_name":"Esra"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"orcid":"0000-0002-1419-3267","first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Research was supported by the Austrian Science Fund (FWF), project I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported by the European Research Council (ERC) CoG 863818 (ForM-SMArt).","date_updated":"2025-11-05T07:34:27Z","publisher":"IEEE","publication_identifier":{"eissn":["2374-9709"],"isbn":["9798350327946"]},"main_file_link":[{"url":"https://schmiste.github.io/noms24.pdf","open_access":"1"}],"oa_version":"Submitted Version","OA_type":"green","publication":"NOMS 2024-2024 IEEE Network Operations and Management Symposium","type":"conference","external_id":{"isi":["001270140300143"]},"publication_status":"published","citation":{"mla":"Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, IEEE, 2024, doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>.","short":"E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024.","ista":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations and Management Symposium. NOMS: Network Operations and Management Symposiu .","ama":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In: <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE; 2024. doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>","chicago":"Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>.","apa":"Ceylan, E., Chatterjee, K., Schmid, S., &#38; Svoboda, J. (2024). Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. Seoul, Republic of Korea: IEEE. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>","ieee":"E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting of network flows: Hardness and an FPT algorithm,” in <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, Seoul, Republic of Korea, 2024."},"language":[{"iso":"eng"}],"date_created":"2025-01-27T15:06:45Z"},{"OA_type":"green","publication":"Indiana University Mathematics Journal","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2112.11150","open_access":"1"}],"type":"journal_article","arxiv":1,"publication_status":"published","external_id":{"arxiv":["2112.11150"]},"citation":{"ieee":"S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness,” <i>Indiana University Mathematics Journal</i>, vol. 73, no. 1. Indiana University Mathematics Journal, pp. 111–148, 2024.","apa":"Hensel, S., &#38; Laux, T. (2024). BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. <i>Indiana University Mathematics Journal</i>. Indiana University Mathematics Journal. <a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">https://doi.org/10.1512/iumj.2024.73.9701</a>","chicago":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” <i>Indiana University Mathematics Journal</i>. Indiana University Mathematics Journal, 2024. <a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">https://doi.org/10.1512/iumj.2024.73.9701</a>.","ama":"Hensel S, Laux T. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. <i>Indiana University Mathematics Journal</i>. 2024;73(1):111-148. doi:<a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">10.1512/iumj.2024.73.9701</a>","ista":"Hensel S, Laux T. 2024. BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics Journal. 73(1), 111–148.","short":"S. Hensel, T. Laux, Indiana University Mathematics Journal 73 (2024) 111–148.","mla":"Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” <i>Indiana University Mathematics Journal</i>, vol. 73, no. 1, Indiana University Mathematics Journal, 2024, pp. 111–48, doi:<a href=\"https://doi.org/10.1512/iumj.2024.73.9701\">10.1512/iumj.2024.73.9701</a>."},"language":[{"iso":"eng"}],"date_created":"2025-01-27T15:20:19Z","volume":73,"date_updated":"2025-01-27T15:23:57Z","publisher":"Indiana University Mathematics Journal","publication_identifier":{"issn":["0022-2518"]},"intvolume":"        73","year":"2024","OA_place":"repository","fulldoi":"https://doi.org/10.1512/iumj.2024.73.9701","article_processing_charge":"No","month":"01","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-7252-8072","first_name":"Sebastian","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"}],"day":"01","page":"111-148","title":"BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness","doi":"10.1512/iumj.2024.73.9701","article_type":"original","scopus_import":"1","abstract":[{"lang":"eng","text":"We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. "}],"_id":"18926","status":"public","oa":1,"corr_author":"1","department":[{"_id":"JuFi"}],"date_published":"2024-01-01T00:00:00Z","quality_controlled":"1"},{"date_updated":"2025-09-09T12:11:33Z","volume":287,"acknowledgement":"Henzinger, Monika: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z 422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020-2024.\r\nSaha, Barna: This project is partially supported by NSF grants 1652303, 1909046, 2112533, and HDR TRIPODS Phase II grant 2217058.\r\nWe would like to thank Andrea Lincoln for many helpful discussions and insightful comments.","publication_identifier":{"isbn":["9783959773096"],"eissn":["1868-8969"]},"alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"arxiv":1,"publication_status":"published","external_id":{"arxiv":["2307.16771"],"isi":["001300389400062"]},"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"15th Innovations in Theoretical Computer Science Conference","OA_type":"gold","oa_version":"Published Version","date_created":"2025-01-27T15:33:42Z","language":[{"iso":"eng"}],"citation":{"ieee":"M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms with predictions for dynamic graph problems,” in <i>15th Innovations in Theoretical Computer Science Conference</i>, Berkeley, CA, United States, 2024, vol. 287, p. 62:1-62:25.","apa":"Henzinger, M., Saha, B., Seybold, M. P., &#38; Ye, C. (2024). On the complexity of algorithms with predictions for dynamic graph problems. In <i>15th Innovations in Theoretical Computer Science Conference</i> (Vol. 287, p. 62:1-62:25). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">https://doi.org/10.4230/LIPIcs.ITCS.2024.62</a>","chicago":"Henzinger, Monika, Barna Saha, Martin P. Seybold, and Christopher Ye. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” In <i>15th Innovations in Theoretical Computer Science Conference</i>, 287:62:1-62:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">https://doi.org/10.4230/LIPIcs.ITCS.2024.62</a>.","ama":"Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with predictions for dynamic graph problems. In: <i>15th Innovations in Theoretical Computer Science Conference</i>. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:62:1-62:25. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">10.4230/LIPIcs.ITCS.2024.62</a>","ista":"Henzinger M, Saha B, Seybold MP, Ye C. 2024. On the complexity of algorithms with predictions for dynamic graph problems. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 287, 62:1-62:25.","short":"M. Henzinger, B. Saha, M.P. Seybold, C. Ye, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25.","mla":"Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” <i>15th Innovations in Theoretical Computer Science Conference</i>, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 62:1-62:25, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.62\">10.4230/LIPIcs.ITCS.2024.62</a>."},"_id":"18928","abstract":[{"lang":"eng","text":"Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.\r\nWe investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.\r\nFurther, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.\r\nWe note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds."}],"status":"public","conference":{"end_date":"2024-02-02","location":"Berkeley, CA, United States","start_date":"2024-01-30","name":"ITCS: Innovations in Theoretical Computer Science"},"scopus_import":"1","doi":"10.4230/LIPIcs.ITCS.2024.62","title":"On the complexity of algorithms with predictions for dynamic graph problems","file":[{"access_level":"open_access","file_size":1084372,"date_updated":"2025-01-27T15:33:24Z","checksum":"15085a5b3697a408b92a4a7a27293927","creator":"dernst","file_id":"18929","content_type":"application/pdf","relation":"main_file","date_created":"2025-01-27T15:33:24Z","file_name":"2024_LIPICs_HenzingerMo.pdf","success":1}],"date_published":"2024-01-24T00:00:00Z","quality_controlled":"1","corr_author":"1","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"department":[{"_id":"MoHe"}],"has_accepted_license":"1","oa":1,"year":"2024","ec_funded":1,"intvolume":"       287","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"24","page":"62:1-62:25","author":[{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"first_name":"Barna","full_name":"Saha, Barna","last_name":"Saha"},{"last_name":"Seybold","full_name":"Seybold, Martin P.","first_name":"Martin P."},{"last_name":"Ye","full_name":"Ye, Christopher","first_name":"Christopher"}],"month":"01","file_date_updated":"2025-01-27T15:33:24Z","article_processing_charge":"Yes","OA_place":"publisher","fulldoi":"https://doi.org/10.4230/LIPIcs.ITCS.2024.62","isi":1},{"has_accepted_license":"1","oa":1,"file":[{"checksum":"d7deb6390f294da69321cfbe352ed611","access_level":"open_access","file_size":1699180,"date_updated":"2025-01-29T08:12:11Z","content_type":"application/pdf","creator":"dernst","file_id":"18935","relation":"main_file","date_created":"2025-01-29T08:12:11Z","file_name":"2024_MolecularBioCell_Sarkany.pdf","success":1}],"quality_controlled":"1","date_published":"2024-03-01T00:00:00Z","department":[{"_id":"FlSc"}],"doi":"10.1091/mbc.e23-07-0289","pmid":1,"title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","abstract":[{"text":"The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .","lang":"eng"}],"_id":"18934","status":"public","article_type":"original","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2025-01-29T08:12:11Z","fulldoi":"https://doi.org/10.1091/mbc.e23-07-0289","OA_place":"publisher","day":"01","author":[{"full_name":"Sárkány, Zsuzsa","last_name":"Sárkány","first_name":"Zsuzsa"},{"full_name":"Figueiredo, Francisco","last_name":"Figueiredo","id":"8125cbe2-9661-11ed-a754-afe96018f37d","first_name":"Francisco"},{"first_name":"Sandra","last_name":"Macedo-Ribeiro","full_name":"Macedo-Ribeiro, Sandra"},{"first_name":"Pedro M.","full_name":"Martins, Pedro M.","last_name":"Martins"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","month":"03","intvolume":"        35","year":"2024","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"publisher":"American Society for Cell Biology","volume":35,"acknowledgement":"We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.","date_updated":"2025-01-29T08:16:20Z","language":[{"iso":"eng"}],"article_number":"mr1","citation":{"mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>.","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024).","ista":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1.","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. 2024;35(3). doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>","chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2024. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>.","apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., &#38; Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>","ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3. American Society for Cell Biology, 2024."},"date_created":"2025-01-29T07:58:40Z","oa_version":"Published Version","OA_type":"hybrid","publication":"Molecular Biology of the Cell","external_id":{"pmid":["38117593"]},"publication_status":"published","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"type":"journal_article"},{"date_created":"2025-01-29T08:33:04Z","citation":{"apa":"Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., &#38; Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. <i>Physica B: Condensed Matter</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physb.2024.416018\">https://doi.org/10.1016/j.physb.2024.416018</a>","ieee":"S. K. Ray <i>et al.</i>, “Tunable magnetoelectronic properties in Bi3+ substituted YCrO3,” <i>Physica B: Condensed Matter</i>, vol. 685. Elsevier, 2024.","ama":"Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. <i>Physica B: Condensed Matter</i>. 2024;685. doi:<a href=\"https://doi.org/10.1016/j.physb.2024.416018\">10.1016/j.physb.2024.416018</a>","chicago":"Ray, Sujata Kumari, Anupama Pati, Payala Sahoo, A.K. Sahoo, Saurabh Singh, Tsunehiro Takeuchi, and S. Dash. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” <i>Physica B: Condensed Matter</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.physb.2024.416018\">https://doi.org/10.1016/j.physb.2024.416018</a>.","short":"S.K. Ray, A. Pati, P. Sahoo, A.K. Sahoo, S. Singh, T. Takeuchi, S. Dash, Physica B: Condensed Matter 685 (2024).","ista":"Ray SK, Pati A, Sahoo P, Sahoo AK, Singh S, Takeuchi T, Dash S. 2024. Tunable magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter. 685, 416018.","mla":"Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted YCrO3.” <i>Physica B: Condensed Matter</i>, vol. 685, 416018, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.physb.2024.416018\">10.1016/j.physb.2024.416018</a>."},"article_number":"416018","language":[{"iso":"eng"}],"type":"journal_article","publication_status":"published","publication":"Physica B: Condensed Matter","OA_type":"closed access","oa_version":"None","publisher":"Elsevier","publication_identifier":{"issn":["0921-4526"]},"date_updated":"2025-01-29T08:37:14Z","acknowledgement":"The authors would like to acknowledge MHRD, Government of India for financial support. The author is also thankful to RRCAT, Indore for providing XPS beamline-14 of Indus II to conduct experimental work.","volume":685,"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","author":[{"last_name":"Ray","full_name":"Ray, Sujata Kumari","first_name":"Sujata Kumari"},{"last_name":"Pati","full_name":"Pati, Anupama","first_name":"Anupama"},{"full_name":"Sahoo, Payala","last_name":"Sahoo","first_name":"Payala"},{"last_name":"Sahoo","full_name":"Sahoo, A.K.","first_name":"A.K."},{"first_name":"Saurabh","last_name":"Singh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269"},{"last_name":"Takeuchi","full_name":"Takeuchi, Tsunehiro","first_name":"Tsunehiro"},{"first_name":"S.","last_name":"Dash","full_name":"Dash, S."}],"fulldoi":"https://doi.org/10.1016/j.physb.2024.416018","article_processing_charge":"No","year":"2024","intvolume":"       685","department":[{"_id":"MaIb"}],"date_published":"2024-07-15T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_type":"original","status":"public","_id":"18937","abstract":[{"lang":"eng","text":"A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions."}],"title":"Tunable magnetoelectronic properties in Bi3+ substituted YCrO3","doi":"10.1016/j.physb.2024.416018"},{"OA_type":"hybrid","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","type":"journal_article","tmp":{"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","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["38289956"]},"publication_status":"published","citation":{"ista":"Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121.","short":"B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>.","ieee":"B. L. Springstein <i>et al.</i>, “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6. National Academy of Sciences, 2024.","apa":"Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>","chicago":"Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>.","ama":"Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(6). doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>"},"article_number":"e2317453121","language":[{"iso":"eng"}],"date_created":"2025-01-29T08:39:27Z","acknowledgement":"We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P.","volume":121,"date_updated":"2025-05-14T11:02:52Z","ddc":["570"],"publisher":"National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":"       121","year":"2024","fulldoi":"https://doi.org/10.1073/pnas.2317453121","OA_place":"publisher","file_date_updated":"2025-01-29T08:43:16Z","article_processing_charge":"No","month":"02","issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-3461-5391","first_name":"Benjamin L","full_name":"Springstein, Benjamin L","last_name":"Springstein","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083"},{"first_name":"Joao A.","full_name":"Paulo, Joao A.","last_name":"Paulo"},{"last_name":"Park","full_name":"Park, Hankum","first_name":"Hankum"},{"first_name":"Kemardo","last_name":"Henry","full_name":"Henry, Kemardo"},{"first_name":"Eleanor","last_name":"Fleming","full_name":"Fleming, Eleanor"},{"last_name":"Feder","full_name":"Feder, Zoë","first_name":"Zoë"},{"first_name":"J. Wade","last_name":"Harper","full_name":"Harper, J. Wade"},{"first_name":"Ann","last_name":"Hochschild","full_name":"Hochschild, Ann"}],"day":"06","title":"Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics","pmid":1,"doi":"10.1073/pnas.2317453121","article_type":"original","scopus_import":"1","_id":"18938","status":"public","abstract":[{"lang":"eng","text":"The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed."}],"oa":1,"has_accepted_license":"1","department":[{"_id":"MaLo"}],"file":[{"date_created":"2025-01-29T08:43:16Z","relation":"main_file","file_name":"2024_PNAS_Springstein.pdf","success":1,"checksum":"5bd62c7cb4287e3706a1d45d6ef61fd1","date_updated":"2025-01-29T08:43:16Z","access_level":"open_access","file_size":720902,"content_type":"application/pdf","file_id":"18939","creator":"dernst"}],"quality_controlled":"1","date_published":"2024-02-06T00:00:00Z"}]