[{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.07259"}],"month":"02","intvolume":" 80","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":80,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2018-07-10","end_date":"2018-07-15","location":"Stockholm, Sweden"},"status":"public","_id":"6012","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T09:50:53Z","publisher":"ML Research Press","quality_controlled":"1","oa":1,"page":"4442-4450","date_published":"2018-02-01T00:00:00Z","date_created":"2019-02-14T15:21:07Z","isi":1,"year":"2018","day":"01","publication":"Proceedings of the 35th International Conference on Machine Learning","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"author":[{"first_name":"Subham","last_name":"Sahoo","full_name":"Sahoo, Subham"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","full_name":"Martius, Georg S"}],"external_id":{"arxiv":["1806.07259"],"isi":["000683379204058"]},"article_processing_charge":"No","title":"Learning equations for extrapolation and control","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.","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.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"6011","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2018-07-15","location":"Stockholm, Sweden","start_date":"2018-07-10"},"type":"conference","status":"public","date_updated":"2023-10-17T09:51:13Z","department":[{"_id":"ChLa"}],"abstract":[{"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. ","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01678"}],"scopus_import":"1","intvolume":" 80","month":"02","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":80,"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"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.","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.","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.","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.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"author":[{"full_name":"Kuzborskij, Ilja","last_name":"Kuzborskij","first_name":"Ilja"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"title":"Data-dependent stability of stochastic gradient descent","oa":1,"publisher":"ML Research Press","quality_controlled":"1","year":"2018","isi":1,"publication":"Proceedings of the 35 th International Conference on Machine Learning","day":"01","page":"2815-2824","date_created":"2019-02-14T14:51:57Z","date_published":"2018-02-01T00:00:00Z"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":"Volume 2018","ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.10505"}],"month":"12","date_updated":"2023-10-17T11:47:20Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"_id":"6589","type":"conference","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02","end_date":"2018-12-08","location":"Montreal, Canada"},"status":"public","isi":1,"year":"2018","day":"01","publication":"Advances in Neural Information Processing Systems 31","page":"5973-5983","date_published":"2018-12-01T00:00:00Z","date_created":"2019-06-27T09:32:55Z","publisher":"Neural Information Processing Systems Foundation","quality_controlled":"1","oa":1,"citation":{"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.","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.","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"first_name":"Mikael","full_name":"Johansson, Mikael","last_name":"Johansson"},{"last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Khirirat","full_name":"Khirirat, Sarit","first_name":"Sarit"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}],"article_processing_charge":"No","external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"title":"The convergence of sparsified gradient methods","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}]},{"date_updated":"2023-10-17T11:50:05Z","department":[{"_id":"SyCr"}],"_id":"7","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["1095-9203"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"6417","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/","description":"News on IST Homepage"}],"record":[{"relation":"research_data","id":"13055","status":"public"}]},"volume":362,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","main_file_link":[{"url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf","open_access":"1"}],"scopus_import":"1","intvolume":" 362","month":"11","citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000451124500041"]},"publist_id":"8049","author":[{"first_name":"Nathalie","full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"last_name":"Crespi","full_name":"Crespi, Alessandro","first_name":"Alessandro"},{"last_name":"Mersch","full_name":"Mersch, Danielle","first_name":"Danielle"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Keller, Laurent","last_name":"Keller","first_name":"Laurent"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"year":"2018","isi":1,"publication":"Science","day":"23","page":"941 - 945","date_created":"2018-12-11T11:44:07Z","doi":"10.1126/science.aat4793","date_published":"2018-11-23T00:00:00Z","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.","oa":1,"publisher":"AAAS","quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"]},"publication_status":"published","volume":35,"issue":"11","pmid":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"08","intvolume":" 35","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"date_updated":"2023-10-17T11:51:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"19","status":"public","type":"journal_article","article_type":"original","day":"28","publication":"Molecular Biology and Evolution","isi":1,"year":"2018","doi":"10.1093/molbev/msy163","date_published":"2018-08-28T00:00:00Z","date_created":"2018-12-11T11:44:11Z","page":"2669 - 2684","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","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.","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."},"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","author":[{"full_name":"Palmer, Adam","last_name":"Palmer","first_name":"Adam"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"publist_id":"8036","external_id":{"isi":["000452567200006"],"pmid":["30169679"]},"article_processing_charge":"No"},{"_id":"6","type":"journal_article","status":"public","date_updated":"2023-10-17T11:49:25Z","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000456469400103"]},"article_processing_charge":"No","publist_id":"8050","author":[{"first_name":"Javier","last_name":"Masís","full_name":"Masís, Javier"},{"first_name":"David","full_name":"Mankus, David","last_name":"Mankus"},{"first_name":"Steffen","full_name":"Wolff, Steffen","last_name":"Wolff"},{"full_name":"Guitchounts, Grigori","last_name":"Guitchounts","first_name":"Grigori"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"department":[{"_id":"MaJö"}],"title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","abstract":[{"text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","publisher":"MyJove Corporation","scopus_import":"1","intvolume":" 141","month":"11","publication_status":"published","year":"2018","isi":1,"publication":"Journal of visualized experiments","language":[{"iso":"eng"}],"day":"08","date_created":"2018-12-11T11:44:07Z","date_published":"2018-11-08T00:00:00Z","volume":141,"doi":"10.3791/58585"},{"status":"public","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"13055","title":"Social network plasticity decreases disease transmission in a eusocial insect","department":[{"_id":"SyCr"}],"author":[{"last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Alessandro","full_name":"Crespi, Alessandro","last_name":"Crespi"},{"last_name":"Mersch","full_name":"Mersch, Danielle","first_name":"Danielle"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Laurent","full_name":"Keller, Laurent","last_name":"Keller"}],"article_processing_charge":"No","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T11:50:04Z","citation":{"mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","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.” Zenodo, 2018.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669","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. Zenodo. https://doi.org/10.5281/ZENODO.1322669","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.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669."},"month":"10","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7"}]},"date_published":"2018-10-23T00:00:00Z","doi":"10.5281/ZENODO.1322669","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2023-05-23T13:24:51Z","day":"23","year":"2018"},{"quality_controlled":"1","oa":1,"date_published":"2018-10-20T00:00:00Z","doi":"10.1364/OPTICA.5.001210","date_created":"2018-12-11T11:44:12Z","page":"1210 - 1219","day":"20","publication":"Optica","isi":1,"year":"2018","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","publist_id":"8033","author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos","first_name":"Kerlos"},{"last_name":"Brown","full_name":"Brown, Elliott","first_name":"Elliott"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"last_name":"Preu","full_name":"Preu, Sascha","first_name":"Sascha"},{"first_name":"Daniel","last_name":"Segovia Vargas","full_name":"Segovia Vargas, Daniel"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"last_name":"Munoz","full_name":"Munoz, Luis","first_name":"Luis"},{"last_name":"Schwefel","full_name":"Schwefel, Harald","first_name":"Harald"}],"article_processing_charge":"No","external_id":{"isi":["000447853100007"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210.","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210"},"month":"10","intvolume":" 5","scopus_import":"1","main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.","lang":"eng"}],"volume":5,"issue":"10","language":[{"iso":"eng"}],"publication_identifier":{"issn":["23342536"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"22","department":[{"_id":"JoFi"}],"date_updated":"2023-10-17T12:12:40Z"},{"date_updated":"2023-10-17T11:53:09Z","department":[{"_id":"ToHe"}],"_id":"5677","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1551-3939"]},"volume":12,"issue":"2-3","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector."}],"intvolume":" 12","month":"05","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053."},"title":"Contracts for system design","article_processing_charge":"No","author":[{"first_name":"Albert","last_name":"Benveniste","full_name":"Benveniste, Albert"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"},{"first_name":"Benoît","full_name":"Caillaud, Benoît","last_name":"Caillaud"},{"last_name":"Passerone","full_name":"Passerone, Roberto","first_name":"Roberto"},{"first_name":"Jean Baptiste","last_name":"Raclet","full_name":"Raclet, Jean Baptiste"},{"first_name":"Philipp","full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier"},{"first_name":"Alberto","last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto"},{"first_name":"Werner","full_name":"Damm, Werner","last_name":"Damm"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Larsen, Kim G.","last_name":"Larsen","first_name":"Kim G."}],"publication":"Foundations and Trends in Electronic Design Automation","day":"01","year":"2018","date_created":"2018-12-16T22:59:19Z","doi":"10.1561/1000000053","date_published":"2018-05-01T00:00:00Z","page":"124-400","oa":1,"publisher":"Now Publishers","quality_controlled":"1"},{"publisher":"Optica Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","doi":"10.1364/OL.43.000607","date_published":"2018-02-01T00:00:00Z","date_created":"2018-12-11T11:46:27Z","page":"607 - 610","day":"01","publication":"Optics Letters","isi":1,"year":"2018","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Coherent-perfect-absorber and laser for bound states in a continuum","author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"publist_id":"7388","external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters. Optica Publishing Group, 2018. https://doi.org/10.1364/OL.43.000607.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 2018;43(3):607-610. doi:10.1364/OL.43.000607","apa":"Midya, B., & Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.43.000607","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” Optics Letters, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” Optics Letters, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:10.1364/OL.43.000607."},"month":"02","intvolume":" 43","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1711.01986","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum."}],"issue":"3","volume":43,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"435","department":[{"_id":"MiLe"}],"date_updated":"2023-10-17T12:15:06Z"},{"article_number":"30083438","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","external_id":{"isi":["000440484800002"]},"article_processing_charge":"No","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"first_name":"Pierre","full_name":"Gagnaire, Pierre","last_name":"Gagnaire"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"publist_id":"7784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018."},"oa":1,"publisher":"PeerJ","quality_controlled":"1","date_created":"2018-12-11T11:44:50Z","doi":"10.7717/peerj.5198","date_published":"2018-07-30T00:00:00Z","publication":"PeerJ","day":"30","year":"2018","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"139","file_date_updated":"2020-07-14T12:44:48Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-10-17T12:25:28Z","intvolume":" 2018","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"issue":"7","volume":2018,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","creator":"dernst","file_size":1480792,"date_updated":"2020-07-14T12:44:48Z","file_name":"2018_PeerJ_Fraisse.pdf","date_created":"2018-12-18T09:42:11Z"}],"publication_status":"published"},{"doi":"10.7717/peerj.5325","date_published":"2018-10-01T00:00:00Z","date_created":"2018-12-11T11:44:16Z","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"PeerJ","quality_controlled":"1","publisher":"PeerJ","oa":1,"acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","publist_id":"8022","author":[{"first_name":"Johanna","full_name":"Bertl, Johanna","last_name":"Bertl"},{"last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michaël","last_name":"Blum","full_name":"Blum, Michaël"}],"article_processing_charge":"No","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","citation":{"chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e5325","volume":2018,"issue":"10","publication_status":"published","file":[{"date_created":"2018-12-17T10:46:06Z","file_name":"2018_PeerJ_Bertl.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:06Z","file_size":1328344,"checksum":"3334886c4b39678db4c4b74299ca14ba","file_id":"5692","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 2018","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"oa_version":"Published Version","pmid":1,"file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"NiBa"}],"date_updated":"2023-10-17T12:24:43Z","ddc":["576"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"33"},{"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"citation":{"mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"article_processing_charge":"No","author":[{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","oa":1,"quality_controlled":"1","publisher":"Nature Research","year":"2018","isi":1,"publication":"Nature Plants","day":"03","page":"1082-1088","date_created":"2018-12-16T22:59:18Z","date_published":"2018-12-03T00:00:00Z","doi":"10.1038/s41477-018-0318-3","_id":"5673","type":"journal_article","status":"public","date_updated":"2023-10-17T12:19:28Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833","open_access":"1"}],"scopus_import":"1","intvolume":" 4","month":"12","publication_status":"published","publication_identifier":{"issn":["2055-0278"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":4,"issue":"12"},{"external_id":{"pmid":["29593089"],"isi":["000428576200023"]},"article_processing_charge":"No","publist_id":"7715","author":[{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"title":"Language acquisition with communication between learners","citation":{"apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"20180073","date_created":"2018-12-11T11:45:09Z","doi":"10.1098/rsif.2018.0073","date_published":"2018-03-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of the Royal Society Interface","day":"01","oa":1,"quality_controlled":"1","publisher":"The Royal Society","file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"KrCh"}],"date_updated":"2023-10-18T06:36:00Z","ddc":["000"],"type":"journal_article","article_type":"original","status":"public","_id":"198","ec_funded":1,"issue":"140","volume":15,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9814"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}]},"publication_status":"published","publication_identifier":{"eissn":["1742-5662"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-12T07:54:37Z","file_name":"2018_RS_IbsenJensen.pdf","date_updated":"2020-07-14T12:45:22Z","file_size":219837,"creator":"dernst","checksum":"444e1a9d98eb0e780671be82b13025f3","file_id":"5955","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":"1","intvolume":" 15","month":"03","abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"oa_version":"Submitted Version","pmid":1},{"article_number":"181286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286"},"title":"Chromatic transitions in the emergence of syntax networks","article_processing_charge":"No","external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra"},{"last_name":"Fibla","full_name":"Fibla, Martí Sànchez","first_name":"Martí Sànchez"},{"first_name":"Sergi","full_name":"Valverde, Sergi","last_name":"Valverde"},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","oa":1,"quality_controlled":"1","publisher":"The Royal Society","publication":"Royal Society Open Science","day":"12","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2019-01-20T22:59:18Z","doi":"10.1098/rsos.181286","date_published":"2018-12-12T00:00:00Z","_id":"5859","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-10-18T06:41:12Z","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"intvolume":" 5","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5924","checksum":"9664d4417f6b792242e31eea77ce9501","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_RoyalSocOS_Corominas.pdf","date_created":"2019-02-05T14:38:09Z","creator":"dernst","file_size":646732,"date_updated":"2020-07-14T12:47:13Z"}],"publication_status":"published","publication_identifier":{"issn":["2054-5703"]},"issue":"12","volume":5},{"status":"public","type":"preprint","article_number":"1804.07752","_id":"6183","department":[{"_id":"LaEr"}],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","article_processing_charge":"No","external_id":{"arxiv":["1804.07752"]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-18T10:46:08Z","citation":{"ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d."},"month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07752"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases."}],"date_created":"2019-03-28T09:20:06Z","related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"},{"status":"public","id":"14694","relation":"later_version"}]},"date_published":"2018-04-20T00:00:00Z","publication":"arXiv","language":[{"iso":"eng"}],"day":"20","year":"2018","publication_status":"submitted"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018).","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057.","chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057."},"date_updated":"2023-12-18T10:51:02Z","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"title":"Convex fair partitions into arbitrary number of pieces","external_id":{"arxiv":["1804.03057"]},"article_processing_charge":"No","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"}],"article_number":"1804.03057","_id":"75","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"preprint","language":[{"iso":"eng"}],"day":"13","year":"2018","publication_status":"published","ec_funded":1,"date_created":"2018-12-11T11:44:30Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8156"}]},"date_published":"2018-09-13T00:00:00Z","doi":"10.48550/arXiv.1804.03057","oa_version":"Preprint","abstract":[{"text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization.","lang":"eng"}],"month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1804.03057","open_access":"1"}],"oa":1,"publisher":"arXiv"},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"citation":{"mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1704.05809"]},"publist_id":"7258","author":[{"full_name":"Betea, Dan","last_name":"Betea","first_name":"Dan"},{"first_name":"Jeremie","last_name":"Bouttier","full_name":"Bouttier, Jeremie"},{"first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter","last_name":"Nejjar"},{"first_name":"Mirjana","full_name":"Vuletic, Mirjana","last_name":"Vuletic"}],"title":"The free boundary Schur process and applications I","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2018","has_accepted_license":"1","publication":"Annales Henri Poincare","day":"13","page":"3663-3742","date_created":"2018-12-11T11:47:09Z","date_published":"2018-11-13T00:00:00Z","doi":"10.1007/s00023-018-0723-1","_id":"556","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2024-02-20T10:48:17Z","ddc":["500"],"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"11","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5866","checksum":"0c38abe73569b7166b7487ad5d23cc68","file_size":3084674,"date_updated":"2020-07-14T12:47:03Z","creator":"dernst","file_name":"2018_Annales_Betea.pdf","date_created":"2019-01-21T15:18:55Z"}],"ec_funded":1,"volume":19,"issue":"12"},{"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"53c17082848e12f3c2e1b4185b578208","file_id":"5600","creator":"system","file_size":1737958,"date_updated":"2020-07-14T12:47:05Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","date_created":"2018-12-12T13:02:34Z"}],"day":"04","datarep_id":"82","year":"2018","has_accepted_license":"1","contributor":[{"contributor_type":"researcher","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2018-12-12T12:31:36Z","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:82","date_published":"2018-01-04T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"Graph matching problems for large displacement optical flow of RGB-D images.","lang":"eng"}],"month":"01","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["001"],"date_updated":"2024-02-21T13:41:17Z","citation":{"mla":"Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:82.","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82","apa":"Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:82","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82.","ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, 10.15479/AT:ISTA:82."},"department":[{"_id":"VlKo"}],"file_date_updated":"2020-07-14T12:47:05Z","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","article_processing_charge":"No","author":[{"first_name":"Hassan","last_name":"Alhaija","full_name":"Alhaija, Hassan"},{"full_name":"Sellent, Anita","last_name":"Sellent","first_name":"Anita"},{"first_name":"Daniel","last_name":"Kondermann","full_name":"Kondermann, Daniel"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"_id":"5573","keyword":["graph matching","quadratic assignment problem<"],"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data"},{"ec_funded":1,"issue":"5","volume":14,"related_material":{"record":[{"id":"5584","status":"public","relation":"research_data"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/","relation":"press_release"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3026f94d235219e15514505fdbadf34e","file_id":"5974","file_size":3460786,"date_updated":"2020-07-14T12:45:53Z","creator":"dernst","file_name":"2018_Plos_Botella_Soler.pdf","date_created":"2019-02-13T11:07:15Z"}],"publication_status":"published","intvolume":" 14","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains."}],"file_date_updated":"2020-07-14T12:45:53Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2024-02-21T13:45:25Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"292","date_created":"2018-12-11T11:45:39Z","doi":"10.1371/journal.pcbi.1006057","date_published":"2018-05-10T00:00:00Z","publication":"PLoS Computational Biology","day":"10","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","title":"Nonlinear decoding of a complex movie from the mammalian retina","article_processing_charge":"Yes","external_id":{"isi":["000434012100002"]},"author":[{"first_name":"Vicent","id":"421234E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicent","last_name":"Botella Soler"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.","ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.","chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057."},"project":[{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270"},{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e1006057"}]