[{"type":"journal_article","issue":"2","abstract":[{"text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space.","lang":"eng"}],"intvolume":" 98","status":"public","title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","_id":"136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"13","citation":{"chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical Society, 2018, doi:10.1103/PhysRevE.98.023105.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical Review E, vol. 98, no. 2. American Physical Society, 2018.","apa":"Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 2018;98(2). doi:10.1103/PhysRevE.98.023105"},"publication":"Physical Review E","date_published":"2018-08-13T00:00:00Z","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2018","volume":98,"date_created":"2018-12-11T11:44:49Z","date_updated":"2023-10-10T13:29:10Z","author":[{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri","first_name":"Balachandra","full_name":"Suri, Balachandra"},{"full_name":"Tithof, Jeffrey","first_name":"Jeffrey","last_name":"Tithof"},{"full_name":"Grigoriev, Roman","first_name":"Roman","last_name":"Grigoriev"},{"first_name":"Michael","last_name":"Schatz","full_name":"Schatz, Michael"}],"month":"08","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1808.02088"],"isi":["000441466800010"]},"main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.98.023105"},{"title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","status":"public","intvolume":" 55","_id":"691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function."}],"issue":"1","article_type":"original","page":"48 - 54","publication":"Journal of Medical Genetics","citation":{"chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group, 2018. https://doi.org/10.1136/jmedgenet-2017-104627.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.","short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54.","apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627","ieee":"I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018.","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54. doi:10.1136/jmedgenet-2017-104627"},"date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"BMJ Publishing Group","year":"2018","pmid":1,"date_created":"2018-12-11T11:47:57Z","date_updated":"2023-10-16T09:55:43Z","volume":55,"author":[{"full_name":"Marin Valencia, Isaac","last_name":"Marin Valencia","first_name":"Isaac"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"last_name":"Johansen","first_name":"Anide","full_name":"Johansen, Anide"},{"last_name":"Rosti","first_name":"Başak","full_name":"Rosti, Başak"},{"full_name":"Issa, Mahmoud","last_name":"Issa","first_name":"Mahmoud"},{"full_name":"Musaev, Damir","first_name":"Damir","last_name":"Musaev"},{"first_name":"Gifty","last_name":"Bhat","full_name":"Bhat, Gifty"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"full_name":"Silhavy, Jennifer","first_name":"Jennifer","last_name":"Silhavy"},{"full_name":"Stanley, Valentina","last_name":"Stanley","first_name":"Valentina"},{"full_name":"Rosti, Rasim","first_name":"Rasim","last_name":"Rosti"},{"full_name":"Gleeson, Jeremy","last_name":"Gleeson","first_name":"Jeremy"},{"last_name":"Imam","first_name":"Farhad","full_name":"Imam, Farhad"},{"full_name":"Zaki, Maha","last_name":"Zaki","first_name":"Maha"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"}],"publist_id":"7016","isi":1,"quality_controlled":"1","project":[{"name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28626029"],"isi":["000418199800007"]},"language":[{"iso":"eng"}],"doi":"10.1136/jmedgenet-2017-104627","month":"01","publication_identifier":{"issn":["0022-2593"]}},{"day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-04T00:00:00Z","publication":"Acta Scientiarum Mathematicarum","citation":{"mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80. doi:10.14232/actasm-018-753-y","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. Springer Nature. https://doi.org/10.14232/actasm-018-753-y","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018."},"article_type":"original","page":"65 - 80","abstract":[{"text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere.","lang":"eng"}],"issue":"1-2","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"284","title":"Maps on probability measures preserving certain distances - a survey and some new results","status":"public","intvolume":" 84","month":"06","publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"doi":"10.14232/actasm-018-753-y","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03305"}],"external_id":{"arxiv":["1802.03305"]},"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"publist_id":"7615","ec_funded":1,"author":[{"full_name":"Virosztek, Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","first_name":"Daniel","last_name":"Virosztek"}],"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-10-16T10:29:22Z","volume":84,"year":"2018","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer Nature"},{"intvolume":" 5","title":"Statistical mechanics of the uniform electron gas","status":"public","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"180","file":[{"relation":"main_file","file_id":"5726","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-17T16:38:18Z","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","access_level":"open_access","file_size":843938,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density.","lang":"eng"}],"page":"79 - 116","article_type":"original","citation":{"chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:10.5802/jep.64.","apa":"Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.64","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64"},"publication":"Journal de l'Ecole Polytechnique - Mathematiques","date_published":"2018-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","department":[{"_id":"RoSe"}],"publisher":"Ecole Polytechnique","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","year":"2018","volume":5,"date_updated":"2023-10-17T08:05:28Z","date_created":"2018-12-11T11:45:03Z","author":[{"last_name":"Lewi","first_name":"Mathieu","full_name":"Lewi, Mathieu"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","publist_id":"7741","ec_funded":1,"file_date_updated":"2020-07-14T12:45:16Z","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"external_id":{"arxiv":["1705.10676"]},"language":[{"iso":"eng"}],"doi":"10.5802/jep.64","publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"month":"07"},{"article_type":"original","page":"903-921","publication":"Journal of Histochemistry and Cytochemistry","citation":{"chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","ieee":"S. Reipert et al., “Agitation modules: Flexible means to accelerate automated freeze substitution,” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE Publications. https://doi.org/10.1369/0022155418786698","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698"},"date_published":"2018-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","status":"public","intvolume":" 66","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"163","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"issue":"12","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1369/0022155418786698","month":"12","publication_identifier":{"issn":["0022-1554"]},"publication_status":"published","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"publisher":"SAGE Publications","year":"2018","pmid":1,"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-10-17T08:42:24Z","volume":66,"author":[{"first_name":"Siegfried","last_name":"Reipert","full_name":"Reipert, Siegfried"},{"last_name":"Goldammer","first_name":"Helmuth","full_name":"Goldammer, Helmuth"},{"last_name":"Richardson","first_name":"Christine","full_name":"Richardson, Christine"},{"first_name":"Martin","last_name":"Goldberg","full_name":"Goldberg, Martin"},{"full_name":"Hawkins, Timothy","last_name":"Hawkins","first_name":"Timothy"},{"last_name":"Hollergschwandtner","first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","full_name":"Hollergschwandtner, Elena"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"last_name":"Antreich","first_name":"Sebastian","full_name":"Antreich, Sebastian"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}]},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-02-01T00:00:00Z","citation":{"short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.","mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450."},"publication":"Proceedings of the 35th International Conference on Machine Learning","page":"4442-4450","abstract":[{"text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"6012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 80","title":"Learning equations for extrapolation and control","status":"public","month":"02","conference":{"name":"ICML: International Conference on Machine Learning","location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1806.07259"],"isi":["000683379204058"]},"main_file_link":[{"url":"https://arxiv.org/abs/1806.07259","open_access":"1"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/"}]},"author":[{"full_name":"Sahoo, Subham","last_name":"Sahoo","first_name":"Subham"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"}],"volume":80,"date_created":"2019-02-14T15:21:07Z","date_updated":"2023-10-17T09:50:53Z","year":"2018","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"publication_status":"published"},{"page":"2815-2824","citation":{"ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018."},"publication":"Proceedings of the 35 th International Conference on Machine Learning","date_published":"2018-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 80","title":"Data-dependent stability of stochastic gradient descent","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6011","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. "}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.01678","open_access":"1"}],"external_id":{"isi":["000683379202095"],"arxiv":["1703.01678"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"month":"02","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"publication_status":"published","year":"2018","volume":80,"date_updated":"2023-10-17T09:51:13Z","date_created":"2019-02-14T14:51:57Z","author":[{"last_name":"Kuzborskij","first_name":"Ilja","full_name":"Kuzborskij, Ilja"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1},{"abstract":[{"text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics.","lang":"eng"}],"type":"conference","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6589","status":"public","title":"The convergence of sparsified gradient methods","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-12-01T00:00:00Z","citation":{"ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., & Renggli, C. (2018). The convergence of sparsified gradient methods. In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in Advances in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: Advances in Neural Information Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” Advances in Neural Information Processing Systems 31, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983."},"publication":"Advances in Neural Information Processing Systems 31","page":"5973-5983","ec_funded":1,"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"},{"full_name":"Johansson, Mikael","first_name":"Mikael","last_name":"Johansson"},{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H"},{"first_name":"Sarit","last_name":"Khirirat","full_name":"Khirirat, Sarit"},{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"}],"volume":"Volume 2018","date_updated":"2023-10-17T11:47:20Z","date_created":"2019-06-27T09:32:55Z","year":"2018","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","month":"12","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-02"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.10505","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1809.10505"],"isi":["000461852000047"]},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1"},{"ec_funded":1,"publist_id":"8049","volume":362,"date_created":"2018-12-11T11:44:07Z","date_updated":"2023-10-17T11:50:05Z","related_material":{"record":[{"id":"13055","status":"public","relation":"research_data"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/"}]},"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"full_name":"Crespi, Alessandro","first_name":"Alessandro","last_name":"Crespi"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Keller, Laurent","last_name":"Keller","first_name":"Laurent"}],"publisher":"AAAS","department":[{"_id":"SyCr"}],"publication_status":"published","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","year":"2018","publication_identifier":{"issn":["1095-9203"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.1126/science.aat4793","project":[{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"external_id":{"isi":["000451124500041"]},"issue":"6417","abstract":[{"text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 362","status":"public","title":"Social network plasticity decreases disease transmission in a eusocial insect","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7","article_processing_charge":"No","day":"23","scopus_import":"1","date_published":"2018-11-23T00:00:00Z","page":"941 - 945","article_type":"original","citation":{"apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Science. AAAS. https://doi.org/10.1126/science.aat4793","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. Science. 2018;362(6417):941-945. doi:10.1126/science.aat4793","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:10.1126/science.aat4793."},"publication":"Science"},{"oa_version":"Submitted Version","status":"public","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","intvolume":" 35","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19","abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"issue":"11","type":"journal_article","date_published":"2018-08-28T00:00:00Z","article_type":"original","page":"2669 - 2684","publication":"Molecular Biology and Evolution","citation":{"ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163."},"day":"28","article_processing_charge":"No","scopus_import":"1","date_created":"2018-12-11T11:44:11Z","date_updated":"2023-10-17T11:51:06Z","volume":35,"author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2018","pmid":1,"publist_id":"8036","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy163","isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"month":"08","publication_identifier":{"issn":["0737-4038"]}}]