[{"intvolume":"         2","status":"public","language":[{"iso":"eng"}],"date_published":"2020-10-01T00:00:00Z","doi":"10.1038/s42256-020-00237-3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":2,"type":"journal_article","isi":1,"month":"10","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","scopus_import":"1","page":"642-652","title":"Neural circuit policies enabling auditable autonomy","external_id":{"isi":["000583337200011"]},"project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publication":"Nature Machine Intelligence","publication_identifier":{"eissn":["2522-5839"]},"day":"01","citation":{"chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” <i>Nature Machine Intelligence</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s42256-020-00237-3\">https://doi.org/10.1038/s42256-020-00237-3</a>.","ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” <i>Nature Machine Intelligence</i>, vol. 2, Springer Nature, 2020, pp. 642–52, doi:<a href=\"https://doi.org/10.1038/s42256-020-00237-3\">10.1038/s42256-020-00237-3</a>.","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., &#38; Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. <i>Nature Machine Intelligence</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42256-020-00237-3\">https://doi.org/10.1038/s42256-020-00237-3</a>","ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” <i>Nature Machine Intelligence</i>, vol. 2. Springer Nature, pp. 642–652, 2020.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. <i>Nature Machine Intelligence</i>. 2020;2:642-652. doi:<a href=\"https://doi.org/10.1038/s42256-020-00237-3\">10.1038/s42256-020-00237-3</a>","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652."},"author":[{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"date_updated":"2023-08-22T10:36:06Z","article_processing_charge":"No","oa_version":"None","quality_controlled":"1","abstract":[{"text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.","lang":"eng"}],"article_type":"original","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-deep-learning-models/"}]},"publication_status":"published","_id":"8679","year":"2020","date_created":"2020-10-19T13:46:06Z"},{"ec_funded":1,"date_created":"2020-10-19T14:09:38Z","year":"2020","_id":"8680","quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","keyword":["Multidisciplinary"],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/sticking-together/"}]},"publication_status":"published","article_type":"original","abstract":[{"text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.","lang":"eng"}],"day":"02","publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"oa":1,"citation":{"short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.aba6637\">https://doi.org/10.1126/science.aba6637</a>.","ieee":"T. Y.-C. Tsai <i>et al.</i>, “An adhesion code ensures robust pattern formation during tissue morphogenesis,” <i>Science</i>, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., &#38; Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aba6637\">https://doi.org/10.1126/science.aba6637</a>","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. <i>Science</i>. 2020;370(6512):113-116. doi:<a href=\"https://doi.org/10.1126/science.aba6637\">10.1126/science.aba6637</a>","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” <i>Science</i>, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:<a href=\"https://doi.org/10.1126/science.aba6637\">10.1126/science.aba6637</a>."},"author":[{"last_name":"Tsai","first_name":"Tony Y.-C.","full_name":"Tsai, Tony Y.-C."},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"first_name":"Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xia, Peng"},{"full_name":"Colak-Champollion, Tugba","last_name":"Colak-Champollion","first_name":"Tugba"},{"full_name":"Knaut, Holger","first_name":"Holger","last_name":"Knaut"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Megason, Sean G.","last_name":"Megason","first_name":"Sean G."}],"date_updated":"2023-08-22T10:36:35Z","issue":"6512","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","external_id":{"isi":["000579169000053"]},"acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant  01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","scopus_import":"1","page":"113-116","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"isi":1,"publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":370,"intvolume":"       370","doi":"10.1126/science.aba6637","date_published":"2020-10-02T00:00:00Z","language":[{"iso":"eng"}],"status":"public"},{"language":[{"iso":"eng"}],"status":"public","doi":"10.1016/j.jde.2020.03.044","date_published":"2020-09-05T00:00:00Z","intvolume":"       269","extern":"1","volume":269,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.04099"}],"page":"4720-4750","arxiv":1,"external_id":{"arxiv":["1909.04099"]},"title":"A KAM theorem for finitely differentiable Hamiltonian systems","issue":"6","date_updated":"2021-01-12T08:20:33Z","citation":{"chicago":"Koudjinan, Edmond. “A KAM Theorem for Finitely Differentiable Hamiltonian Systems.” <i>Journal of Differential Equations</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jde.2020.03.044\">https://doi.org/10.1016/j.jde.2020.03.044</a>.","ista":"Koudjinan E. 2020. A KAM theorem for finitely differentiable Hamiltonian systems. Journal of Differential Equations. 269(6), 4720–4750.","mla":"Koudjinan, Edmond. “A KAM Theorem for Finitely Differentiable Hamiltonian Systems.” <i>Journal of Differential Equations</i>, vol. 269, no. 6, Elsevier, 2020, pp. 4720–50, doi:<a href=\"https://doi.org/10.1016/j.jde.2020.03.044\">10.1016/j.jde.2020.03.044</a>.","ieee":"E. Koudjinan, “A KAM theorem for finitely differentiable Hamiltonian systems,” <i>Journal of Differential Equations</i>, vol. 269, no. 6. Elsevier, pp. 4720–4750, 2020.","apa":"Koudjinan, E. (2020). A KAM theorem for finitely differentiable Hamiltonian systems. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2020.03.044\">https://doi.org/10.1016/j.jde.2020.03.044</a>","ama":"Koudjinan E. A KAM theorem for finitely differentiable Hamiltonian systems. <i>Journal of Differential Equations</i>. 2020;269(6):4720-4750. doi:<a href=\"https://doi.org/10.1016/j.jde.2020.03.044\">10.1016/j.jde.2020.03.044</a>","short":"E. Koudjinan, Journal of Differential Equations 269 (2020) 4720–4750."},"author":[{"id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","full_name":"Koudjinan, Edmond","orcid":"0000-0003-2640-4049","last_name":"Koudjinan","first_name":"Edmond"}],"publication_identifier":{"issn":["0022-0396"]},"publication":"Journal of Differential Equations","oa":1,"day":"05","abstract":[{"lang":"eng","text":"Given l>2ν>2d≥4, we prove the persistence of a Cantor--family of KAM tori of measure O(ε1/2−ν/l) for any non--degenerate nearly integrable Hamiltonian system of class Cl(D×Td), where D⊂Rd is a bounded domain, provided that the size ε of the perturbation is sufficiently small. This extends a result by D. Salamon in \\cite{salamon2004kolmogorov} according to which we do have the persistence of a single KAM torus in the same framework. Moreover, it is well--known that, for the persistence of a single torus, the regularity assumption can not be improved."}],"publication_status":"published","article_type":"original","oa_version":"Preprint","keyword":["Analysis"],"article_processing_charge":"No","quality_controlled":"1","year":"2020","_id":"8691","date_created":"2020-10-21T15:03:05Z"},{"date_created":"2020-10-21T15:43:05Z","year":"2020","_id":"8694","quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"We develop algorithms and techniques to compute rigorous bounds for finite pieces of orbits of the critical points, for intervals of parameter values, in the quadratic family of one-dimensional maps fa(x)=a−x2. We illustrate the effectiveness of our approach by constructing a dynamically defined partition 𝒫 of the parameter interval Ω=[1.4,2] into almost 4×106 subintervals, for each of which we compute to high precision the orbits of the critical points up to some time N and other dynamically relevant quantities, several of which can vary greatly, possibly spanning several orders of magnitude. We also subdivide 𝒫 into a family 𝒫+ of intervals, which we call stochastic intervals, and a family 𝒫− of intervals, which we call regular intervals. We numerically prove that each interval ω∈𝒫+ has an escape time, which roughly means that some iterate of the critical point taken over all the parameters in ω has considerable width in the phase space. This suggests, in turn, that most parameters belonging to the intervals in 𝒫+ are stochastic and most parameters belonging to the intervals in 𝒫− are regular, thus the names. We prove that the intervals in 𝒫+ occupy almost 90% of the total measure of Ω. The software and the data are freely available at http://www.pawelpilarczyk.com/quadr/, and a web page is provided for carrying out the calculations. The ideas and procedures can be easily generalized to apply to other parameterized families of dynamical systems."}],"day":"31","publication":"Chaos","oa":1,"citation":{"short":"A. Golmakani, E. Koudjinan, S. Luzzatto, P. Pilarczyk, Chaos 30 (2020).","mla":"Golmakani, Ali, et al. “Rigorous Numerics for Critical Orbits in the Quadratic Family.” <i>Chaos</i>, vol. 30, no. 7, 073143, AIP, 2020, doi:<a href=\"https://doi.org/10.1063/5.0012822\">10.1063/5.0012822</a>.","ieee":"A. Golmakani, E. Koudjinan, S. Luzzatto, and P. Pilarczyk, “Rigorous numerics for critical orbits in the quadratic family,” <i>Chaos</i>, vol. 30, no. 7. AIP, 2020.","ama":"Golmakani A, Koudjinan E, Luzzatto S, Pilarczyk P. Rigorous numerics for critical orbits in the quadratic family. <i>Chaos</i>. 2020;30(7). doi:<a href=\"https://doi.org/10.1063/5.0012822\">10.1063/5.0012822</a>","apa":"Golmakani, A., Koudjinan, E., Luzzatto, S., &#38; Pilarczyk, P. (2020). Rigorous numerics for critical orbits in the quadratic family. <i>Chaos</i>. AIP. <a href=\"https://doi.org/10.1063/5.0012822\">https://doi.org/10.1063/5.0012822</a>","chicago":"Golmakani, Ali, Edmond Koudjinan, Stefano Luzzatto, and Pawel Pilarczyk. “Rigorous Numerics for Critical Orbits in the Quadratic Family.” <i>Chaos</i>. AIP, 2020. <a href=\"https://doi.org/10.1063/5.0012822\">https://doi.org/10.1063/5.0012822</a>.","ista":"Golmakani A, Koudjinan E, Luzzatto S, Pilarczyk P. 2020. Rigorous numerics for critical orbits in the quadratic family. Chaos. 30(7), 073143."},"author":[{"first_name":"Ali","last_name":"Golmakani","full_name":"Golmakani, Ali"},{"first_name":"Edmond","last_name":"Koudjinan","orcid":"0000-0003-2640-4049","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E"},{"full_name":"Luzzatto, Stefano","first_name":"Stefano","last_name":"Luzzatto"},{"full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk"}],"date_updated":"2021-01-12T08:20:34Z","article_number":"073143","issue":"7","title":"Rigorous numerics for critical orbits in the quadratic family","external_id":{"arxiv":["2004.13444"]},"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/2004.13444","open_access":"1"}],"publisher":"AIP","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":30,"intvolume":"        30","extern":"1","doi":"10.1063/5.0012822","date_published":"2020-07-31T00:00:00Z","language":[{"iso":"eng"}],"status":"public"},{"_id":"8695","year":"2020","date_created":"2020-10-23T09:08:28Z","page":"36","article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group \"Open Science Strategy\" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.","lang":"eng"},{"text":"Der Blick auf internationale Aktivitäten zu Open Science zeigt ein breites Spektrum von einzelnen institutionellen Policies bis hin zu nationalen Aktionsplänen. Die vorliegenden Empfehlungen für eine nationale Open Science Strategie in Österreich orientieren sich an diesen internationalen Initiativen und stellen praktische Überlegungen für ihre koordinierte Implementierung im Hinblick auf strategische Entwicklungen in Forschung, Technologie und Innovation (FTI) bis 2030 in Österreich dar. Dabei richten sie sich an alle relevanten Akteur*innen im FTI System, im Besonderen an Forschungsstätten, Forschungsförderer, Forschungspolitik, Gedächtnisinstitutionen wie Bibliotheken und Wissenschafter*innen. Das Empfehlungspapier wurde von 2018 bis 2020 von der OANA-Arbeitsgruppe \"Open Science Strategie\" entwickelt und im Frühling 2020 das erste Mal für eine öffentliche Konsultation veröffentlicht. Die nun vorliegende finale Version des Empfehlungsdokuments, die Feedback und Kommentare aus der Konsultation enthält, soll ein Anstoß für die weitere Diskussion und Umsetzung von Open Science in Österreich sein und als Beitrag und Grundlage einer potentiellen nationalen Open Science Strategie in Österreich dienen. Das Dokument baut auf der vielfältigen Expertise der Autor*innen auf (Wissenschaft, Administration, Bibliothek und Archiv, Informationstechnologie, Wissenschaftspolitik, Förderwesen etc.) und spiegelt deren persönliche Erfahrungen und Meinung wider.","lang":"ger"}],"file":[{"date_updated":"2020-10-23T09:29:45Z","file_name":"2020_OANA_Mayer.pdf","file_id":"8696","relation":"main_file","date_created":"2020-10-23T09:29:45Z","success":1,"access_level":"open_access","creator":"dernst","checksum":"8eba912bb4b20b4f82f8010f2110461a","content_type":"application/pdf","file_size":2298363}],"month":"10","publication_status":"published","publisher":"OANA","department":[{"_id":"E-Lib"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-10-23T09:29:45Z","day":"21","author":[{"first_name":"Katja","last_name":"Mayer","full_name":"Mayer, Katja"},{"full_name":"Rieck, Katharina","last_name":"Rieck","first_name":"Katharina"},{"first_name":"Stefan","last_name":"Reichmann","full_name":"Reichmann, Stefan"},{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","last_name":"Danowski","first_name":"Patrick"},{"last_name":"Graschopf","first_name":"Anton","full_name":"Graschopf, Anton"},{"full_name":"König, Thomas","last_name":"König","first_name":"Thomas"},{"full_name":"Kraker, Peter","first_name":"Peter","last_name":"Kraker"},{"full_name":"Lehner, Patrick","first_name":"Patrick","last_name":"Lehner"},{"full_name":"Reckling, Falk","last_name":"Reckling","first_name":"Falk"},{"full_name":"Ross-Hellauer, Tony","first_name":"Tony","last_name":"Ross-Hellauer"},{"full_name":"Spichtinger, Daniel","first_name":"Daniel","last_name":"Spichtinger"},{"full_name":"Tzatzanis, Michalis","first_name":"Michalis","last_name":"Tzatzanis"},{"last_name":"Schürz","first_name":"Stefanie","full_name":"Schürz, Stefanie"}],"type":"working_paper","date_updated":"2020-10-23T09:34:40Z","citation":{"short":"K. Mayer, K. Rieck, S. Reichmann, P. Danowski, A. Graschopf, T. König, P. Kraker, P. Lehner, F. Reckling, T. Ross-Hellauer, D. Spichtinger, M. Tzatzanis, S. Schürz, Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 2020.","ista":"Mayer K, Rieck K, Reichmann S, Danowski P, Graschopf A, König T, Kraker P, Lehner P, Reckling F, Ross-Hellauer T, Spichtinger D, Tzatzanis M, Schürz S. 2020. Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria, OANA, 36p.","chicago":"Mayer, Katja, Katharina Rieck, Stefan Reichmann, Patrick Danowski, Anton Graschopf, Thomas König, Peter Kraker, et al. <i>Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria</i>. OANA, 2020. <a href=\"https://doi.org/10.5281/ZENODO.4109242\">https://doi.org/10.5281/ZENODO.4109242</a>.","ieee":"K. Mayer <i>et al.</i>, <i>Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria</i>. OANA, 2020.","apa":"Mayer, K., Rieck, K., Reichmann, S., Danowski, P., Graschopf, A., König, T., … Schürz, S. (2020). <i>Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria</i>. OANA. <a href=\"https://doi.org/10.5281/ZENODO.4109242\">https://doi.org/10.5281/ZENODO.4109242</a>","ama":"Mayer K, Rieck K, Reichmann S, et al. <i>Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria</i>. OANA; 2020. doi:<a href=\"https://doi.org/10.5281/ZENODO.4109242\">10.5281/ZENODO.4109242</a>","mla":"Mayer, Katja, et al. <i>Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria</i>. OANA, 2020, doi:<a href=\"https://doi.org/10.5281/ZENODO.4109242\">10.5281/ZENODO.4109242</a>."},"ddc":["020"],"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)"},"status":"public","title":"Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria","language":[{"iso":"ger"}],"date_published":"2020-10-21T00:00:00Z","doi":"10.5281/ZENODO.4109242"},{"year":"2020","_id":"8697","date_created":"2020-10-25T23:01:16Z","file":[{"file_size":1223899,"content_type":"application/pdf","checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","access_level":"open_access","creator":"cziletti","file_id":"8710","success":1,"date_created":"2020-10-27T12:09:57Z","relation":"main_file","file_name":"2020_Nonlinearity_Fischer.pdf","date_updated":"2020-10-27T12:09:57Z"}],"abstract":[{"lang":"eng","text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","author":[{"first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Kniely","full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333"}],"citation":{"ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” <i>Nonlinearity</i>, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","apa":"Fischer, J. L., &#38; Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/ab9728\">https://doi.org/10.1088/1361-6544/ab9728</a>","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. <i>Nonlinearity</i>. 2020;33(11):5733-5772. doi:<a href=\"https://doi.org/10.1088/1361-6544/ab9728\">10.1088/1361-6544/ab9728</a>","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” <i>Nonlinearity</i>, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:<a href=\"https://doi.org/10.1088/1361-6544/ab9728\">10.1088/1361-6544/ab9728</a>.","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” <i>Nonlinearity</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6544/ab9728\">https://doi.org/10.1088/1361-6544/ab9728</a>.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772."},"date_updated":"2023-08-22T10:38:38Z","publication":"Nonlinearity","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"oa":1,"day":"01","external_id":{"arxiv":["1906.12245"],"isi":["000576492700001"]},"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","issue":"11","has_accepted_license":"1","page":"5733-5772","arxiv":1,"scopus_import":"1","publisher":"IOP Publishing","department":[{"_id":"JuFi"}],"month":"11","isi":1,"volume":33,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-10-27T12:09:57Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"status":"public","doi":"10.1088/1361-6544/ab9728","date_published":"2020-11-01T00:00:00Z","intvolume":"        33","ddc":["510"]},{"citation":{"mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:<a href=\"https://doi.org/10.1073/pnas.1912804117\">10.1073/pnas.1912804117</a>.","apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., &#38; Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. <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.1912804117\">https://doi.org/10.1073/pnas.1912804117</a>","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(40):25066-25073. doi:<a href=\"https://doi.org/10.1073/pnas.1912804117\">10.1073/pnas.1912804117</a>","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1912804117\">https://doi.org/10.1073/pnas.1912804117</a>.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073."},"date_updated":"2023-08-22T12:11:23Z","author":[{"last_name":"Maoz","first_name":"Ori","full_name":"Maoz, Ori"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"first_name":"Mohamad Saleh","last_name":"Esteki","full_name":"Esteki, Mohamad Saleh"},{"first_name":"Roozbeh","last_name":"Kiani","full_name":"Kiani, Roozbeh"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"}],"oa":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"day":"06","external_id":{"isi":["000579045200012"],"pmid":["32948691"]},"title":"Learning probabilistic neural representations with randomly connected circuits","issue":"40","has_accepted_license":"1","_id":"8698","year":"2020","date_created":"2020-10-25T23:01:16Z","pmid":1,"abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"file":[{"file_size":1755359,"content_type":"application/pdf","checksum":"c6a24fdecf3f28faf447078e7a274a88","access_level":"open_access","creator":"cziletti","file_id":"8713","date_created":"2020-10-27T14:57:50Z","relation":"main_file","success":1,"file_name":"2020_PNAS_Maoz.pdf","date_updated":"2020-10-27T14:57:50Z"}],"publication_status":"published","article_type":"original","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","volume":117,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-10-27T14:57:50Z","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"date_published":"2020-10-06T00:00:00Z","doi":"10.1073/pnas.1912804117","ddc":["570"],"intvolume":"       117","page":"25066-25073","scopus_import":"1","acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","month":"10","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"isi":1},{"article_type":"original","publication_status":"published","file":[{"date_updated":"2020-10-28T11:53:12Z","relation":"main_file","date_created":"2020-10-28T11:53:12Z","success":1,"file_id":"8715","file_name":"2020_PNAS_Paris.pdf","creator":"cziletti","access_level":"open_access","file_size":1176522,"content_type":"application/pdf","checksum":"1638fa36b442e2868576c6dd7d6dc505"}],"abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","ec_funded":1,"date_created":"2020-10-25T23:01:17Z","pmid":1,"year":"2020","_id":"8699","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000579059100029"],"pmid":["32958669"],"arxiv":["2009.12262"]},"title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","has_accepted_license":"1","issue":"40","citation":{"ieee":"E. Paris <i>et al.</i>, “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(40):24764-24770. doi:<a href=\"https://doi.org/10.1073/pnas.2012043117\">10.1073/pnas.2012043117</a>","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. <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.2012043117\">https://doi.org/10.1073/pnas.2012043117</a>","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:<a href=\"https://doi.org/10.1073/pnas.2012043117\">10.1073/pnas.2012043117</a>.","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2012043117\">https://doi.org/10.1073/pnas.2012043117</a>.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770."},"date_updated":"2023-08-22T12:11:52Z","author":[{"last_name":"Paris","first_name":"Eugenio","full_name":"Paris, Eugenio"},{"first_name":"Yi","last_name":"Tseng","full_name":"Tseng, Yi"},{"orcid":"0000-0003-0853-8182","id":"8275014E-6063-11E9-9B7F-6338E6697425","full_name":"Paerschke, Ekaterina","last_name":"Paerschke","first_name":"Ekaterina"},{"first_name":"Wenliang","last_name":"Zhang","full_name":"Zhang, Wenliang"},{"full_name":"Upton, Mary H","last_name":"Upton","first_name":"Mary H"},{"first_name":"Anna","last_name":"Efimenko","full_name":"Efimenko, Anna"},{"full_name":"Rolfs, Katharina","last_name":"Rolfs","first_name":"Katharina"},{"full_name":"McNally, Daniel E","last_name":"McNally","first_name":"Daniel E"},{"full_name":"Maurel, Laura","last_name":"Maurel","first_name":"Laura"},{"last_name":"Naamneh","first_name":"Muntaser","full_name":"Naamneh, Muntaser"},{"first_name":"Marco","last_name":"Caputo","full_name":"Caputo, Marco"},{"full_name":"Strocov, Vladimir N","first_name":"Vladimir N","last_name":"Strocov"},{"full_name":"Wang, Zhiming","last_name":"Wang","first_name":"Zhiming"},{"full_name":"Casa, Diego","first_name":"Diego","last_name":"Casa"},{"full_name":"Schneider, Christof W","first_name":"Christof W","last_name":"Schneider"},{"full_name":"Pomjakushina, Ekaterina","first_name":"Ekaterina","last_name":"Pomjakushina"},{"full_name":"Wohlfeld, Krzysztof","last_name":"Wohlfeld","first_name":"Krzysztof"},{"first_name":"Milan","last_name":"Radovic","full_name":"Radovic, Milan"},{"first_name":"Thorsten","last_name":"Schmitt","full_name":"Schmitt, Thorsten"}],"day":"06","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","oa":1,"department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","month":"10","isi":1,"arxiv":1,"page":"24764-24770","acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","scopus_import":"1","doi":"10.1073/pnas.2012043117","date_published":"2020-10-06T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","intvolume":"       117","ddc":["530"],"type":"journal_article","volume":117,"file_date_updated":"2020-10-28T11:53:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_updated":"2023-08-22T10:39:38Z","citation":{"short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>.","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. 2020;54(5):739-748. doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molecular Biology</i>, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>."},"author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr"},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"full_name":"Shuvalov, A. V.","first_name":"A. V.","last_name":"Shuvalov"},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}],"publication":"Molecular Biology","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"day":"01","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","external_id":{"isi":["000579441200009"]},"issue":"5","year":"2020","_id":"8700","date_created":"2020-10-25T23:01:17Z","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"publication_status":"published","article_type":"original","related_material":{"record":[{"relation":"original","status":"public","id":"8701"}]},"oa_version":"None","article_processing_charge":"No","quality_controlled":"1","volume":54,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","doi":"10.1134/S0026893320050088","date_published":"2020-09-01T00:00:00Z","intvolume":"        54","page":"739-748","scopus_import":"1","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"month":"09","isi":1},{"language":[{"iso":"rus"}],"status":"public","doi":"10.31857/S0026898420050080","date_published":"2020-09-01T00:00:00Z","intvolume":"        54","volume":54,"type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Russian Academy of Sciences","department":[{"_id":"FyKo"}],"month":"09","page":"837-848","scopus_import":"1","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","external_id":{"pmid":["33009793"]},"issue":"5","author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr"},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"first_name":"A. V.","last_name":"Shuvalov","full_name":"Shuvalov, A. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"citation":{"ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>.","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. 2020;54(5):837-848. doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848."},"date_updated":"2023-08-22T10:39:37Z","publication_identifier":{"issn":["00268984"]},"publication":"Molekuliarnaia biologiia","day":"01","abstract":[{"text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"8700","relation":"translation"}]},"article_type":"original","publication_status":"published","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","year":"2020","_id":"8701","date_created":"2020-10-25T23:01:17Z","pmid":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-10-27T14:31:52Z","volume":173,"type":"conference","intvolume":"       173","ddc":["000"],"alternative_title":["LIPIcs"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_published":"2020-08-26T00:00:00Z","doi":"10.4230/LIPIcs.ESA.2020.75","scopus_import":"1","conference":{"name":"ESA: Annual European Symposium on Algorithms","start_date":"2020-09-07","location":"Virtual, Online; Pisa, Italy","end_date":"2020-09-09"},"month":"08","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"oa":1,"publication_identifier":{"isbn":["9783959771627"],"issn":["18688969"]},"publication":"28th Annual European Symposium on Algorithms","day":"26","date_updated":"2023-09-07T13:29:00Z","citation":{"short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","mla":"Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” <i>28th Annual European Symposium on Algorithms</i>, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2020.75\">10.4230/LIPIcs.ESA.2020.75</a>.","ieee":"G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in <i>28th Annual European Symposium on Algorithms</i>, Virtual, Online; Pisa, Italy, 2020, vol. 173.","ama":"Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: <i>28th Annual European Symposium on Algorithms</i>. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2020.75\">10.4230/LIPIcs.ESA.2020.75</a>","apa":"Osang, G. F., Rouxel-Labbé, M., &#38; Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In <i>28th Annual European Symposium on Algorithms</i> (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2020.75\">https://doi.org/10.4230/LIPIcs.ESA.2020.75</a>","chicago":"Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In <i>28th Annual European Symposium on Algorithms</i>, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2020.75\">https://doi.org/10.4230/LIPIcs.ESA.2020.75</a>.","ista":"Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75."},"author":[{"last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"},{"last_name":"Rouxel-Labbé","first_name":"Mael","full_name":"Rouxel-Labbé, Mael"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"article_number":"75","has_accepted_license":"1","title":"Generalizing CGAL periodic Delaunay triangulations","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"_id":"8703","year":"2020","date_created":"2020-10-25T23:01:18Z","ec_funded":1,"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. ","lang":"eng"}],"file":[{"checksum":"fe0f7c49a99ed870c671b911e10d5496","file_size":733291,"content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2020_LIPIcs_Osang.pdf","success":1,"date_created":"2020-10-27T14:31:52Z","relation":"main_file","file_id":"8712","date_updated":"2020-10-27T14:31:52Z"}],"publication_status":"published","related_material":{"record":[{"id":"9056","status":"public","relation":"dissertation_contains"}]}},{"doi":"10.1109/ICRA40945.2020.9196608","date_published":"2020-05-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","alternative_title":["ICRA"],"ddc":["000"],"type":"conference","file_date_updated":"2020-11-06T10:58:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"}],"publisher":"IEEE","month":"05","isi":1,"page":"5446-5452","conference":{"end_date":"2020-08-31","location":"Paris, France","start_date":"2020-05-31","name":"ICRA: International Conference on Robotics and Automation"},"acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","scopus_import":"1","project":[{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000712319503110"]},"title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","has_accepted_license":"1","date_updated":"2023-08-22T10:40:15Z","citation":{"short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, 5446–52. IEEE, 2020. <a href=\"https://doi.org/10.1109/ICRA40945.2020.9196608\">https://doi.org/10.1109/ICRA40945.2020.9196608</a>.","ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: <i>Proceedings - IEEE International Conference on Robotics and Automation</i>. IEEE; 2020:5446-5452. doi:<a href=\"https://doi.org/10.1109/ICRA40945.2020.9196608\">10.1109/ICRA40945.2020.9196608</a>","apa":"Lechner, M., Hasani, R., Rus, D., &#38; Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In <i>Proceedings - IEEE International Conference on Robotics and Automation</i> (pp. 5446–5452). Paris, France: IEEE. <a href=\"https://doi.org/10.1109/ICRA40945.2020.9196608\">https://doi.org/10.1109/ICRA40945.2020.9196608</a>","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Paris, France, 2020, pp. 5446–5452.","mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, IEEE, 2020, pp. 5446–52, doi:<a href=\"https://doi.org/10.1109/ICRA40945.2020.9196608\">10.1109/ICRA40945.2020.9196608</a>."},"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"day":"01","publication_identifier":{"isbn":["9781728173955"],"issn":["10504729"]},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","oa":1,"publication_status":"published","file":[{"file_size":1070010,"content_type":"application/pdf","checksum":"fccf7b986ac78046918a298cc6849a50","creator":"dernst","access_level":"open_access","date_created":"2020-11-06T10:58:49Z","success":1,"relation":"main_file","file_id":"8733","file_name":"2020_ICRA_Lechner.pdf","date_updated":"2020-11-06T10:58:49Z"}],"abstract":[{"text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.","lang":"eng"}],"quality_controlled":"1","oa_version":"Submitted Version","article_processing_charge":"No","date_created":"2020-10-25T23:01:19Z","year":"2020","_id":"8704"},{"date_created":"2020-10-25T23:01:19Z","ec_funded":1,"_id":"8705","year":"2020","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","id":"11473","status":"public"}]},"publication_status":"published","abstract":[{"lang":"eng","text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model."}],"file":[{"creator":"cziletti","access_level":"open_access","file_size":469831,"content_type":"application/pdf","checksum":"c12c9c1e6f08def245e42f3cb1d83827","date_updated":"2020-10-27T12:49:04Z","date_created":"2020-10-27T12:49:04Z","success":1,"relation":"main_file","file_id":"8711","file_name":"2020_Annales_Mysliwy.pdf"}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","citation":{"ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” <i>Annales Henri Poincare</i>, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. <i>Annales Henri Poincare</i>. 2020;21(12):4003-4025. doi:<a href=\"https://doi.org/10.1007/s00023-020-00969-3\">10.1007/s00023-020-00969-3</a>","apa":"Mysliwy, K., &#38; Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-020-00969-3\">https://doi.org/10.1007/s00023-020-00969-3</a>","mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” <i>Annales Henri Poincare</i>, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:<a href=\"https://doi.org/10.1007/s00023-020-00969-3\">10.1007/s00023-020-00969-3</a>.","ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025.","chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” <i>Annales Henri Poincare</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00023-020-00969-3\">https://doi.org/10.1007/s00023-020-00969-3</a>.","short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025."},"author":[{"last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"date_updated":"2023-09-07T13:43:51Z","day":"01","oa":1,"publication":"Annales Henri Poincare","publication_identifier":{"issn":["1424-0637"]},"external_id":{"isi":["000578111800002"],"arxiv":["2003.12371"]},"title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"has_accepted_license":"1","issue":"12","arxiv":1,"page":"4003-4025","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","scopus_import":"1","month":"12","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"isi":1,"type":"journal_article","volume":21,"file_date_updated":"2020-10-27T12:49:04Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s00023-020-00969-3","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)"},"status":"public","language":[{"iso":"eng"}],"intvolume":"        21","ddc":["530"]},{"page":"278-284","scopus_import":"1","month":"07","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","department":[{"_id":"E-Lib"}],"type":"journal_article","volume":73,"file_date_updated":"2020-10-27T16:27:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-14T00:00:00Z","doi":"10.31263/voebm.v73i2.3941","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)"},"status":"public","language":[{"iso":"ger"}],"intvolume":"        73","ddc":["020"],"date_created":"2020-10-25T23:01:19Z","_id":"8706","year":"2020","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level."},{"text":"Als Teil des Hochschulraumstrukturmittel-Projekts Austrian Transition to Open Access (AT2OA) befasst sich das Teilprojekt TP1-B mit der Konzeption einer Monitoring-Lösung für den Open Access-Publikationsoutput in Österreich. Der nun vorliegende Bericht zu einem potentiellen Open Access-Monitoring in Österreich ist eines der Ergebnisse dieser Bemühungen und kann als Grundlage einer Diskussion auf internationaler Ebene dienen.","lang":"ger"}],"file":[{"date_updated":"2020-10-27T16:27:25Z","file_name":"2020_VOEB_Danowski.pdf","file_id":"8714","relation":"main_file","date_created":"2020-10-27T16:27:25Z","success":1,"access_level":"open_access","creator":"kschuh","checksum":"37443c34d91d5bdbeb38c78b14792537","content_type":"application/pdf","file_size":960317}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2021-01-12T08:20:40Z","author":[{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski"},{"full_name":"Ferus, Andreas","first_name":"Andreas","last_name":"Ferus"},{"first_name":"Anna-Laetitia","last_name":"Hikl","full_name":"Hikl, Anna-Laetitia"},{"full_name":"McNeill, Gerda","last_name":"McNeill","first_name":"Gerda"},{"full_name":"Miniberger, Clemens","last_name":"Miniberger","first_name":"Clemens"},{"full_name":"Reding, Steve","first_name":"Steve","last_name":"Reding"},{"full_name":"Zarka, Tobias","last_name":"Zarka","first_name":"Tobias"},{"full_name":"Zojer, Michael","first_name":"Michael","last_name":"Zojer"}],"citation":{"chicago":"Danowski, Patrick, Andreas Ferus, Anna-Laetitia Hikl, Gerda McNeill, Clemens Miniberger, Steve Reding, Tobias Zarka, and Michael Zojer. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. <a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">https://doi.org/10.31263/voebm.v73i2.3941</a>.","ista":"Danowski P, Ferus A, Hikl A-L, McNeill G, Miniberger C, Reding S, Zarka T, Zojer M. 2020. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(2), 278–284.","mla":"Danowski, Patrick, et al. “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 2, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 278–84, doi:<a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">10.31263/voebm.v73i2.3941</a>.","ieee":"P. Danowski <i>et al.</i>, “„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 2. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 278–284, 2020.","apa":"Danowski, P., Ferus, A., Hikl, A.-L., McNeill, G., Miniberger, C., Reding, S., … Zojer, M. (2020). „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">https://doi.org/10.31263/voebm.v73i2.3941</a>","ama":"Danowski P, Ferus A, Hikl A-L, et al. „Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2020;73(2):278-284. doi:<a href=\"https://doi.org/10.31263/voebm.v73i2.3941\">10.31263/voebm.v73i2.3941</a>","short":"P. Danowski, A. Ferus, A.-L. Hikl, G. McNeill, C. Miniberger, S. Reding, T. Zarka, M. Zojer, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 278–284."},"day":"14","oa":1,"publication_identifier":{"eissn":["10222588"]},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","title":"„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B","has_accepted_license":"1","issue":"2"},{"_id":"8707","year":"2020","pmid":1,"date_created":"2020-10-25T23:01:20Z","abstract":[{"text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.","lang":"eng"}],"publication_status":"published","article_type":"original","article_processing_charge":"No","oa_version":"None","quality_controlled":"1","date_updated":"2023-08-22T10:37:10Z","citation":{"chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>.","ieee":"S.  Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” <i>Nature Genetics</i>, vol. 52. Springer Nature, pp. 1247–1255, 2020.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>","short":"S.  Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255."},"author":[{"full_name":" Galan, Silvia","first_name":"Silvia","last_name":" Galan"},{"orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N","last_name":"Machnik"},{"full_name":"Kruse, Kai","last_name":"Kruse","first_name":"Kai"},{"first_name":"Noelia","last_name":"Díaz","full_name":"Díaz, Noelia"},{"full_name":"Marti-Renom, Marc A","first_name":"Marc A","last_name":"Marti-Renom"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"publication_identifier":{"eissn":["15461718"],"issn":["10614036"]},"publication":"Nature Genetics","day":"19","external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","page":"1247-1255","scopus_import":"1","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","month":"10","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","isi":1,"volume":52,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","language":[{"iso":"eng"}],"date_published":"2020-10-19T00:00:00Z","doi":"10.1038/s41588-020-00712-y","intvolume":"        52"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":370,"type":"journal_article","intvolume":"       370","status":"public","language":[{"iso":"eng"}],"date_published":"2020-10-30T00:00:00Z","doi":"10.1126/science.aba3178","scopus_import":"1","acknowledgement":"We acknowledge M. Glanc and Y. Zhang for providing entryclones; Vienna Biocenter Core Facilities (VBCF) for recombinantprotein production and purification; Vienna Biocenter Massspectrometry Facility, Bioimaging, and Life Science Facilities at IST Austria and Proteomics Core Facility CEITEC for a great assistance.Funding:This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 742985) and Austrian Science Fund (FWF): I 3630-B25 to J.F.and by grants from the Austrian Academy of Science through the Gregor Mendel Institute (Y.B.) and the Austrian Agency for International Cooperation in Education and Research (D.D.); the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001) (W.S.); the Research Foundation–Flanders (FWO;Odysseus II G0D0515N) and a European Research Council grant (ERC; StG TORPEDO; 714055) to B.D.R., B.Y., and E.M.; and the Hertha Firnberg Programme postdoctoral fellowship (T-947) from the FWF Austrian Science Fund to E.S.-L.; J.H. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at IST Austria.","page":"550-557","main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/MED/33122378#free-full-text"}],"isi":1,"month":"10","department":[{"_id":"JiFr"}],"publisher":"American Association for the Advancement of Science","oa":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication":"Science","day":"30","citation":{"short":"J. Hajny, T. Prat, N. Rydza, L. Rodriguez Solovey, S. Tan, I. Verstraeten, D. Domjan, E. Mazur, E. Smakowska-Luzan, W. Smet, E. Mor, J. Nolf, B. Yang, W. Grunewald, G. Molnar, Y. Belkhadir, B. De Rybel, J. Friml, Science 370 (2020) 550–557.","apa":"Hajny, J., Prat, T., Rydza, N., Rodriguez Solovey, L., Tan, S., Verstraeten, I., … Friml, J. (2020). Receptor kinase module targets PIN-dependent auxin transport during canalization. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aba3178\">https://doi.org/10.1126/science.aba3178</a>","ieee":"J. Hajny <i>et al.</i>, “Receptor kinase module targets PIN-dependent auxin transport during canalization,” <i>Science</i>, vol. 370, no. 6516. American Association for the Advancement of Science, pp. 550–557, 2020.","ama":"Hajny J, Prat T, Rydza N, et al. Receptor kinase module targets PIN-dependent auxin transport during canalization. <i>Science</i>. 2020;370(6516):550-557. doi:<a href=\"https://doi.org/10.1126/science.aba3178\">10.1126/science.aba3178</a>","mla":"Hajny, Jakub, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” <i>Science</i>, vol. 370, no. 6516, American Association for the Advancement of Science, 2020, pp. 550–57, doi:<a href=\"https://doi.org/10.1126/science.aba3178\">10.1126/science.aba3178</a>.","ista":"Hajny J, Prat T, Rydza N, Rodriguez Solovey L, Tan S, Verstraeten I, Domjan D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnar G, Belkhadir Y, De Rybel B, Friml J. 2020. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science. 370(6516), 550–557.","chicago":"Hajny, Jakub, Tomas Prat, N Rydza, Lesia Rodriguez Solovey, Shutang Tan, Inge Verstraeten, David Domjan, et al. “Receptor Kinase Module Targets PIN-Dependent Auxin Transport during Canalization.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.aba3178\">https://doi.org/10.1126/science.aba3178</a>."},"date_updated":"2023-09-05T12:02:35Z","author":[{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas"},{"full_name":"Rydza, N","last_name":"Rydza","first_name":"N"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge"},{"first_name":"David","last_name":"Domjan","orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","full_name":"Domjan, David"},{"full_name":"Mazur, E","last_name":"Mazur","first_name":"E"},{"first_name":"E","last_name":"Smakowska-Luzan","full_name":"Smakowska-Luzan, E"},{"first_name":"W","last_name":"Smet","full_name":"Smet, W"},{"full_name":"Mor, E","first_name":"E","last_name":"Mor"},{"full_name":"Nolf, J","first_name":"J","last_name":"Nolf"},{"first_name":"B","last_name":"Yang","full_name":"Yang, B"},{"last_name":"Grunewald","first_name":"W","full_name":"Grunewald, W"},{"last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","last_name":"Belkhadir","full_name":"Belkhadir, Y"},{"first_name":"B","last_name":"De Rybel","full_name":"De Rybel, B"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"issue":"6516","external_id":{"pmid":["33122378"],"isi":["000583031800041"]},"title":"Receptor kinase module targets PIN-dependent auxin transport during canalization","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","grant_number":"25239","_id":"2699E3D2-B435-11E9-9278-68D0E5697425"}],"_id":"8721","year":"2020","ec_funded":1,"pmid":1,"date_created":"2020-11-02T10:04:46Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization."}],"publication_status":"published","article_type":"original","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/molecular-compass-for-cell-orientation/","relation":"press_release"}]}},{"conference":{"start_date":"2020-02-22","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"San Diego, CA, United States","end_date":"2020-02-26"},"page":"45-61","arxiv":1,"department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","month":"02","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.04207","open_access":"1"}],"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","doi":"10.1145/3332466.3374528","date_published":"2020-02-01T00:00:00Z","year":"2020","_id":"8722","ec_funded":1,"date_created":"2020-11-05T15:25:30Z","abstract":[{"lang":"eng","text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy."}],"publication_status":"published","oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","date_updated":"2023-08-22T12:13:48Z","author":[{"last_name":"Li","first_name":"Shigang","full_name":"Li, Shigang"},{"full_name":"Tal Ben-Nun, Tal Ben-Nun","last_name":"Tal Ben-Nun","first_name":"Tal Ben-Nun"},{"full_name":"Girolamo, Salvatore Di","first_name":"Salvatore Di","last_name":"Girolamo"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"}],"citation":{"chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In <i>Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 45–61. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3332466.3374528\">https://doi.org/10.1145/3332466.3374528</a>.","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” <i>Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2020, pp. 45–61, doi:<a href=\"https://doi.org/10.1145/3332466.3374528\">10.1145/3332466.3374528</a>.","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in <i>Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Diego, CA, United States, 2020, pp. 45–61.","ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: <i>Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2020:45-61. doi:<a href=\"https://doi.org/10.1145/3332466.3374528\">10.1145/3332466.3374528</a>","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., &#38; Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In <i>Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3332466.3374528\">https://doi.org/10.1145/3332466.3374528</a>","short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61."},"publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","oa":1,"day":"01","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"external_id":{"isi":["000564476500004"],"arxiv":["1908.04207"]},"title":"Taming unbalanced training workloads in deep learning with partial collective operations"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-02-15T09:00:01Z","volume":119,"type":"conference","ddc":["000"],"intvolume":"       119","status":"public","language":[{"iso":"eng"}],"date_published":"2020-07-12T00:00:00Z","scopus_import":"1","acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","page":"5416-5425","conference":{"location":"Online","start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning","end_date":"2020-07-18"},"arxiv":1,"month":"07","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"ML Research Press","oa":1,"publication":"Proceedings of the 37th International Conference on Machine Learning","publication_identifier":{"issn":["2640-3498"]},"day":"12","citation":{"short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, ML Research Press, 2020, pp. 5416–25.","ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ML Research Press; 2020:5416-5425.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., &#38; Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 5416–5425). Online: ML Research Press.","ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Online, 2020, vol. 119, pp. 5416–5425.","chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:5416–25. ML Research Press, 2020.","ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425."},"date_updated":"2023-09-07T13:42:08Z","author":[{"last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Frantar","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"},{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"has_accepted_license":"1","external_id":{"arxiv":["2002.10384"]},"title":"On the sample complexity of adversarial multi-source PAC learning","project":[{"name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223"}],"_id":"8724","year":"2020","date_created":"2020-11-05T15:25:58Z","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. ","lang":"eng"}],"file":[{"file_id":"9120","date_created":"2021-02-15T09:00:01Z","success":1,"relation":"main_file","file_name":"2020_PMLR_Konstantinov.pdf","date_updated":"2021-02-15T09:00:01Z","file_size":281286,"content_type":"application/pdf","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","access_level":"open_access","creator":"dernst"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"10799","status":"public"}],"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}]}},{"acknowledgement":"Vitaly Aksenov: Government of Russian Federation (Grant 08-08).\r\nDan Alistarh: ERC Starting Grant 805223 ScaleML.","arxiv":1,"conference":{"end_date":"2020-10-16","location":"Freiburg, Germany","start_date":"2020-10-12","name":"DISC: Symposium on Distributed Computing"},"page":"3:1-3:18","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"month":"08","file_date_updated":"2021-03-11T12:33:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":179,"ddc":["000"],"intvolume":"       179","doi":"10.4230/LIPIcs.DISC.2020.3","date_published":"2020-08-03T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"ec_funded":1,"date_created":"2020-11-05T15:26:17Z","series_title":"LIPIcs","year":"2020","_id":"8725","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","file":[{"access_level":"open_access","creator":"dernst","checksum":"a626a9c47df52b6f6d97edd910dae4ba","file_size":740358,"content_type":"application/pdf","date_updated":"2021-03-11T12:33:35Z","file_name":"2020_LIPIcs_Aksenov.pdf","file_id":"9237","relation":"main_file","date_created":"2021-03-11T12:33:35Z","success":1}],"abstract":[{"lang":"eng","text":"The design and implementation of efficient concurrent data structures have\r\nseen significant attention. However, most of this work has focused on\r\nconcurrent data structures providing good \\emph{worst-case} guarantees. In real\r\nworkloads, objects are often accessed at different rates, since access\r\ndistributions may be non-uniform. Efficient distribution-adaptive data\r\nstructures are known in the sequential case, e.g. the splay-trees; however,\r\nthey often are hard to translate efficiently in the concurrent case.\r\n  In this paper, we investigate distribution-adaptive concurrent data\r\nstructures and propose a new design called the splay-list. At a high level, the\r\nsplay-list is similar to a standard skip-list, with the key distinction that\r\nthe height of each element adapts dynamically to its access rate: popular\r\nelements ``move up,'' whereas rarely-accessed elements decrease in height. We\r\nshow that the splay-list provides order-optimal amortized complexity bounds for\r\na subset of operations while being amenable to efficient concurrent\r\nimplementation. Experimental results show that the splay-list can leverage\r\ndistribution-adaptivity to improve on the performance of classic concurrent\r\ndesigns, and can outperform the only previously-known distribution-adaptive\r\ndesign in certain settings."}],"day":"03","publication":"34th International Symposium on Distributed Computing","publication_identifier":{"isbn":["9783959771689"],"issn":["1868-8969"]},"oa":1,"author":[{"full_name":"Aksenov, Vitaly","first_name":"Vitaly","last_name":"Aksenov"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Alexandra","last_name":"Drozdova","full_name":"Drozdova, Alexandra"},{"full_name":"Mohtashami, Amirkeivan","first_name":"Amirkeivan","last_name":"Mohtashami"}],"date_updated":"2023-02-23T13:41:40Z","citation":{"short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 3:1-3:18.","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2020. The splay-list: A distribution-adaptive concurrent skip-list. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed ComputingLIPIcs vol. 179, 3:1-3:18.","chicago":"Aksenov, Vitaly, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” In <i>34th International Symposium on Distributed Computing</i>, 179:3:1-3:18. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.3\">https://doi.org/10.4230/LIPIcs.DISC.2020.3</a>.","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” in <i>34th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2020, vol. 179, p. 3:1-3:18.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. In: <i>34th International Symposium on Distributed Computing</i>. Vol 179. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:3:1-3:18. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.3\">10.4230/LIPIcs.DISC.2020.3</a>","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., &#38; Mohtashami, A. (2020). The splay-list: A distribution-adaptive concurrent skip-list. In <i>34th International Symposium on Distributed Computing</i> (Vol. 179, p. 3:1-3:18). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.3\">https://doi.org/10.4230/LIPIcs.DISC.2020.3</a>","mla":"Aksenov, Vitaly, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” <i>34th International Symposium on Distributed Computing</i>, vol. 179, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 3:1-3:18, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2020.3\">10.4230/LIPIcs.DISC.2020.3</a>."},"has_accepted_license":"1","project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"The splay-list: A distribution-adaptive concurrent skip-list","external_id":{"arxiv":["2008.01009"]}},{"article_number":"53","issue":"3","has_accepted_license":"1","title":"Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling","external_id":{"arxiv":["2009.11773"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa":1,"publication_identifier":{"issn":["2410-3896"]},"publication":"Condensed Matter","day":"26","author":[{"first_name":"Dorota","last_name":"Gotfryd","full_name":"Gotfryd, Dorota"},{"first_name":"Ekaterina","last_name":"Paerschke","orcid":"0000-0003-0853-8182","id":"8275014E-6063-11E9-9B7F-6338E6697425","full_name":"Paerschke, Ekaterina"},{"first_name":"Krzysztof","last_name":"Wohlfeld","full_name":"Wohlfeld, Krzysztof"},{"full_name":"Oleś, Andrzej M.","last_name":"Oleś","first_name":"Andrzej M."}],"citation":{"short":"D. Gotfryd, E. Paerschke, K. Wohlfeld, A.M. Oleś, Condensed Matter 5 (2020).","chicago":"Gotfryd, Dorota, Ekaterina Paerschke, Krzysztof Wohlfeld, and Andrzej M. Oleś. “Evolution of Spin-Orbital Entanglement with Increasing Ising Spin-Orbit Coupling.” <i>Condensed Matter</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/condmat5030053\">https://doi.org/10.3390/condmat5030053</a>.","ista":"Gotfryd D, Paerschke E, Wohlfeld K, Oleś AM. 2020. Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling. Condensed Matter. 5(3), 53.","mla":"Gotfryd, Dorota, et al. “Evolution of Spin-Orbital Entanglement with Increasing Ising Spin-Orbit Coupling.” <i>Condensed Matter</i>, vol. 5, no. 3, 53, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/condmat5030053\">10.3390/condmat5030053</a>.","ieee":"D. Gotfryd, E. Paerschke, K. Wohlfeld, and A. M. Oleś, “Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling,” <i>Condensed Matter</i>, vol. 5, no. 3. MDPI, 2020.","ama":"Gotfryd D, Paerschke E, Wohlfeld K, Oleś AM. Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling. <i>Condensed Matter</i>. 2020;5(3). doi:<a href=\"https://doi.org/10.3390/condmat5030053\">10.3390/condmat5030053</a>","apa":"Gotfryd, D., Paerschke, E., Wohlfeld, K., &#38; Oleś, A. M. (2020). Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling. <i>Condensed Matter</i>. MDPI. <a href=\"https://doi.org/10.3390/condmat5030053\">https://doi.org/10.3390/condmat5030053</a>"},"date_updated":"2021-01-12T08:20:46Z","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Several realistic spin-orbital models for transition metal oxides go beyond the classical expectations and could be understood only by employing the quantum entanglement. Experiments on these materials confirm that spin-orbital entanglement has measurable consequences. Here, we capture the essential features of spin-orbital entanglement in complex quantum matter utilizing 1D spin-orbital model which accommodates SU(2)⊗SU(2) symmetric Kugel-Khomskii superexchange as well as the Ising on-site spin-orbit coupling. Building on the results obtained for full and effective models in the regime of strong spin-orbit coupling, we address the question whether the entanglement found on superexchange bonds always increases when the Ising spin-orbit coupling is added. We show that (i) quantum entanglement is amplified by strong spin-orbit coupling and, surprisingly, (ii) almost classical disentangled states are possible. We complete the latter case by analyzing how the entanglement existing for intermediate values of spin-orbit coupling can disappear for higher values of this coupling.","lang":"eng"}],"file":[{"file_name":"2020_CondensedMatter_Gotfryd.pdf","relation":"main_file","date_created":"2020-11-06T07:24:40Z","success":1,"file_id":"8727","date_updated":"2020-11-06T07:24:40Z","checksum":"a57a698ff99a11b6665bafd1bac7afbc","content_type":"application/pdf","file_size":768336,"creator":"dernst","access_level":"open_access"}],"publication_status":"published","article_type":"original","_id":"8726","year":"2020","ec_funded":1,"date_created":"2020-11-06T07:21:00Z","intvolume":"         5","ddc":["530"],"status":"public","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"}],"date_published":"2020-08-26T00:00:00Z","doi":"10.3390/condmat5030053","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-11-06T07:24:40Z","volume":5,"type":"journal_article","month":"08","department":[{"_id":"MiLe"}],"publisher":"MDPI","scopus_import":"1","arxiv":1}]