[{"abstract":[{"lang":"eng","text":"Multi-exit architectures, in which a stack of processing layers is interleaved with early output layers, allow the processing of a test example to stop early and thus save computation time and/or energy.  In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments  on  CIFAR100  and  ImageNet  show  that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy  for  late  ones.   The  method  is  particularly  beneficial when  training  data  is  limited  and  it  allows  a  straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time."}],"publication":"IEEE International Conference on Computer Vision","date_published":"2019-10-01T00:00:00Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","scopus_import":"1","date_created":"2020-02-11T09:06:57Z","type":"conference","volume":"2019-October","department":[{"_id":"ChLa"}],"quality_controlled":"1","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","publisher":"IEEE","page":"1355-1364","_id":"7479","language":[{"iso":"eng"}],"author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"file":[{"content_type":"application/pdf","creator":"bphuong","checksum":"7b77fb5c2d27c4c37a7612ba46a66117","file_name":"main.pdf","relation":"main_file","file_id":"7480","file_size":735768,"date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-11T09:06:39Z","access_level":"open_access"}],"month":"10","file_date_updated":"2020-07-14T12:47:59Z","ddc":["000"],"citation":{"chicago":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” In <i>IEEE International Conference on Computer Vision</i>, 2019–October:1355–64. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCV.2019.00144\">https://doi.org/10.1109/ICCV.2019.00144</a>.","ieee":"M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,” in <i>IEEE International Conference on Computer Vision</i>, Seoul, Korea, 2019, vol. 2019–October, pp. 1355–1364.","short":"M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision, IEEE, 2019, pp. 1355–1364.","mla":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” <i>IEEE International Conference on Computer Vision</i>, vol. 2019–October, IEEE, 2019, pp. 1355–64, doi:<a href=\"https://doi.org/10.1109/ICCV.2019.00144\">10.1109/ICCV.2019.00144</a>.","ama":"Phuong M, Lampert C. Distillation-based training for multi-exit architectures. In: <i>IEEE International Conference on Computer Vision</i>. Vol 2019-October. IEEE; 2019:1355-1364. doi:<a href=\"https://doi.org/10.1109/ICCV.2019.00144\">10.1109/ICCV.2019.00144</a>","ista":"Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures. IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision vol. 2019–October, 1355–1364.","apa":"Phuong, M., &#38; Lampert, C. (2019). Distillation-based training for multi-exit architectures. In <i>IEEE International Conference on Computer Vision</i> (Vol. 2019–October, pp. 1355–1364). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2019.00144\">https://doi.org/10.1109/ICCV.2019.00144</a>"},"conference":{"location":"Seoul, Korea","name":"ICCV: International Conference on Computer Vision","start_date":"2019-10-27","end_date":"2019-11-02"},"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"9418","relation":"dissertation_contains"}]},"ec_funded":1,"year":"2019","article_processing_charge":"No","oa":1,"doi":"10.1109/ICCV.2019.00144","title":"Distillation-based training for multi-exit architectures","external_id":{"isi":["000531438101047"]},"isi":1,"day":"01","publication_identifier":{"isbn":["9781728148038"],"issn":["15505499"]},"date_updated":"2023-09-08T11:11:12Z"},{"month":"02","author":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"},{"orcid":"0000-0002-8696-6978","full_name":"Kutzer, Megan","last_name":"Kutzer","first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","citation":{"ama":"Cremer S, Kutzer M. Social immunity. In: Choe J, ed. <i>Encyclopedia of Animal Behavior</i>. 2nd ed. Elsevier; 2019:747-755. doi:<a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">10.1016/B978-0-12-809633-8.90721-0</a>","apa":"Cremer, S., &#38; Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), <i>Encyclopedia of Animal Behavior</i> (2nd ed., pp. 747–755). Elsevier. <a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>","ista":"Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior. , 747–755.","ieee":"S. Cremer and M. Kutzer, “Social immunity,” in <i>Encyclopedia of Animal Behavior</i>, 2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.","chicago":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In <i>Encyclopedia of Animal Behavior</i>, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. <a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>.","short":"S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior, 2nd ed., Elsevier, 2019, pp. 747–755.","mla":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” <i>Encyclopedia of Animal Behavior</i>, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:<a href=\"https://doi.org/10.1016/B978-0-12-809633-8.90721-0\">10.1016/B978-0-12-809633-8.90721-0</a>."},"date_created":"2020-02-23T23:00:36Z","edition":"2","scopus_import":"1","status":"public","date_published":"2019-02-06T00:00:00Z","publication":"Encyclopedia of Animal Behavior","abstract":[{"lang":"eng","text":"Social insects (i.e., ants, termites and the social bees and wasps) protect their colonies from disease using a combination of individual immunity and collectively performed defenses, termed social immunity. The first line of social immune defense is sanitary care, which is performed by colony members to protect their pathogen-exposed nestmates from developing an infection. If sanitary care fails and an infection becomes established, a second line of social immune defense is deployed to stop disease transmission within the colony and to protect the valuable queens, which together with the males are the reproductive individuals of the colony. Insect colonies are separated into these reproductive individuals and the sterile worker force, forming a superorganismal reproductive unit reminiscent of the differentiated germline and soma in a multicellular organism. Ultimately, the social immune response preserves the germline of the superorganism insect colony and increases overall fitness of the colony in case of disease. "}],"page":"747-755","language":[{"iso":"eng"}],"_id":"7513","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"external_id":{"isi":["000248989500026"]},"quality_controlled":"1","department":[{"_id":"SyCr"}],"title":"Social immunity","editor":[{"last_name":"Choe","first_name":"Jae","full_name":"Choe, Jae"}],"doi":"10.1016/B978-0-12-809633-8.90721-0","publisher":"Elsevier","date_updated":"2023-09-08T11:12:04Z","publication_status":"published","publication_identifier":{"isbn":["9780128132517"],"eisbn":["9780128132524"]},"day":"06","year":"2019","article_processing_charge":"No","type":"book_chapter"},{"language":[{"iso":"eng"}],"_id":"7524","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv:1910.03372","date_published":"2019-10-08T00:00:00Z","status":"public","page":"61","abstract":[{"lang":"eng","text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."}],"citation":{"apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:1910.03372</i>. ArXiv.","ista":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372, .","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:191003372</i>.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>, ArXiv.","short":"A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>arXiv:1910.03372</i>. ArXiv.","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>. ArXiv, n.d."},"date_created":"2020-02-26T08:46:40Z","scopus_import":1,"author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert"},{"full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","last_name":"Mayer","first_name":"Simon"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"oa_version":"Preprint","month":"10","oa":1,"article_processing_charge":"No","type":"preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.03372"}],"year":"2019","ec_funded":1,"related_material":{"record":[{"status":"public","id":"7790","relation":"later_version"},{"status":"public","id":"7514","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T13:12:41Z","publisher":"ArXiv","day":"08","publication_status":"draft","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"}],"department":[{"_id":"RoSe"}],"title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound"},{"project":[{"call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","main_file_link":[{"url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks","open_access":"1"}],"volume":32,"type":"conference","oa_version":"Published Version","date_created":"2020-02-28T10:03:24Z","status":"public","date_published":"2019-12-01T00:00:00Z","abstract":[{"text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs.","lang":"eng"}],"intvolume":"        32","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"external_id":{"isi":["000534424300084"],"arxiv":["1909.02253"]},"title":"Powerset convolutional neural networks","date_updated":"2023-09-08T11:13:52Z","publication_identifier":{"issn":["1049-5258"]},"day":"01","year":"2019","ec_funded":1,"conference":{"location":"Vancouver, Canada","name":"NIPS: Conference on Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14"},"article_processing_charge":"No","oa":1,"month":"12","author":[{"last_name":"Wendler","first_name":"Chris","full_name":"Wendler, Chris"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Püschel, Markus","first_name":"Markus","last_name":"Püschel"}],"citation":{"ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","apa":"Wendler, C., Alistarh, D.-A., &#38; Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.","ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019.","mla":"Wendler, Chris, et al. <i>Powerset Convolutional Neural Networks</i>. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.","short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938."},"arxiv":1,"page":"927-938","language":[{"iso":"eng"}],"_id":"7542"},{"external_id":{"pmid":["31519744"]},"title":"Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans","doi":"10.1534/g3.119.400654","date_updated":"2021-01-12T08:14:07Z","publication_identifier":{"issn":["2160-1836"]},"day":"01","year":"2019","article_processing_charge":"No","month":"11","author":[{"first_name":"Jesse","last_name":"Cohn","full_name":"Cohn, Jesse"},{"last_name":"Dwivedi","first_name":"Vivek","full_name":"Dwivedi, Vivek"},{"first_name":"Giulio","last_name":"Valperga","full_name":"Valperga, Giulio"},{"full_name":"Zarate, Nicole","last_name":"Zarate","first_name":"Nicole"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"},{"full_name":"Horvitz, H. Robert","last_name":"Horvitz","first_name":"H. Robert"},{"first_name":"Jonathan T.","last_name":"Pierce","full_name":"Pierce, Jonathan T."}],"citation":{"short":"J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T. Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.","mla":"Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14, doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>.","ieee":"J. Cohn <i>et al.</i>, “Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11. Genetics Society of America, pp. 3703–3714, 2019.","chicago":"Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono, H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>.","apa":"Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., &#38; Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>","ista":"Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. 2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 9(11), 3703–3714.","ama":"Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. 2019;9(11):3703-3714. doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>"},"article_type":"original","issue":"11","page":"3703-3714","_id":"7547","language":[{"iso":"eng"}],"pmid":1,"quality_controlled":"1","publisher":"Genetics Society of America","publication_status":"published","volume":9,"type":"journal_article","oa_version":"Published Version","date_created":"2020-02-28T10:44:27Z","extern":"1","status":"public","date_published":"2019-11-01T00:00:00Z","publication":"G3: Genes, Genomes, Genetics","abstract":[{"text":"The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms.","lang":"eng"}],"intvolume":"         9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","author":[{"full_name":"Sinnige, Tessa","last_name":"Sinnige","first_name":"Tessa"},{"first_name":"Prashanth","last_name":"Ciryam","full_name":"Ciryam, Prashanth"},{"first_name":"Samuel","last_name":"Casford","full_name":"Casford, Samuel"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"}],"month":"05","article_number":"e0217746","extern":"1","article_type":"original","citation":{"chicago":"Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson, Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>.","ieee":"T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo, “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response,” <i>PLOS ONE</i>, vol. 14, no. 5. Public Library of Science, 2019.","mla":"Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>.","short":"T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo, PLOS ONE 14 (2019).","ama":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. 2019;14(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>","ista":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.","apa":"Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., &#38; Vendruscolo, M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>"},"date_created":"2020-02-28T10:45:13Z","abstract":[{"text":"Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity.","lang":"eng"}],"publication":"PLOS ONE","issue":"5","date_published":"2019-05-31T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"7548","intvolume":"        14","doi":"10.1371/journal.pone.0217746","title":"Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response","quality_controlled":"1","day":"31","publication_identifier":{"issn":["1932-6203"]},"publication_status":"published","date_updated":"2021-01-12T08:14:08Z","publisher":"Public Library of Science","year":"2019","type":"journal_article","volume":14,"article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1910.10050"}],"type":"journal_article","volume":28,"department":[{"_id":"JaMa"}],"quality_controlled":"1","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"publication_status":"published","publisher":"Gakko Tosho","abstract":[{"text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ","lang":"eng"}],"publication":"Advances in Mathematical Sciences and Applications","date_published":"2019-10-22T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        28","oa_version":"Preprint","date_created":"2020-02-28T10:54:41Z","year":"2019","oa":1,"article_processing_charge":"No","title":"Penalization via global functionals of optimal-control problems for dissipative evolution","external_id":{"arxiv":["1910.10050"]},"day":"22","publication_identifier":{"issn":["1343-4373"]},"date_updated":"2022-06-17T07:52:41Z","page":"425-447","issue":"2","language":[{"iso":"eng"}],"_id":"7550","acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","author":[{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"},{"full_name":"Stefanelli, Ulisse","first_name":"Ulisse","last_name":"Stefanelli"}],"month":"10","article_type":"original","citation":{"ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. 2019;28(2):425-447.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447.","apa":"Portinale, L., &#38; Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho.","chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho, 2019.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447."},"arxiv":1},{"citation":{"ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. <i>arXiv:191208579</i>.","apa":"Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. <i>arXiv:1912.08579</i>. ArXiv.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” <i>arXiv:1912.08579</i>. ArXiv.","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>. ArXiv, n.d.","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>, ArXiv.","short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.)."},"date_created":"2020-02-28T10:57:08Z","arxiv":1,"month":"12","oa_version":"Preprint","author":[{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7552","language":[{"iso":"eng"}],"abstract":[{"text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ","lang":"eng"}],"page":"5","date_published":"2019-12-18T00:00:00Z","status":"public","publication":"arXiv:1912.08579","publication_status":"submitted","day":"18","publisher":"ArXiv","date_updated":"2021-01-12T08:14:09Z","department":[{"_id":"GaTk"}],"title":"Action at a distance in transcriptional regulation","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"external_id":{"arxiv":["1912.08579"]},"type":"preprint","oa":1,"article_processing_charge":"No","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08579"}]},{"publisher":"EasyChair Publications","publication_status":"published","quality_controlled":"1","department":[{"_id":"ToHe"}],"volume":61,"type":"conference","date_created":"2020-03-08T23:00:49Z","scopus_import":1,"oa_version":"Published Version","intvolume":"        61","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2019-05-25T00:00:00Z","publication":"EPiC Series in Computing","abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"date_updated":"2021-01-12T08:14:17Z","publication_identifier":{"eissn":["23987340"]},"day":"25","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","doi":"10.29007/m75b","oa":1,"article_processing_charge":"No","year":"2019","has_accepted_license":"1","conference":{"start_date":"2019-04-15","end_date":"2019-04-15","location":"Montreal, Canada","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"citation":{"ieee":"F. Immler <i>et al.</i>, “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, Montreal, Canada, 2019, vol. 61, pp. 41–61.","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 61:41–61. EasyChair Publications, 2019. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>.","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>.","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 61. EasyChair Publications; 2019:41-61. doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61."},"ddc":["000"],"month":"05","file_date_updated":"2020-07-14T12:48:00Z","author":[{"full_name":"Immler, Fabian","first_name":"Fabian","last_name":"Immler"},{"last_name":"Althoff","first_name":"Matthias","full_name":"Althoff, Matthias"},{"full_name":"Benet, Luis","last_name":"Benet","first_name":"Luis"},{"full_name":"Chapoutot, Alexandre","first_name":"Alexandre","last_name":"Chapoutot"},{"full_name":"Chen, Xin","last_name":"Chen","first_name":"Xin"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"first_name":"Luca","last_name":"Geretti","full_name":"Geretti, Luca"},{"full_name":"Kochdumper, Niklas","last_name":"Kochdumper","first_name":"Niklas"},{"first_name":"David P.","last_name":"Sanders","full_name":"Sanders, David P."},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling"}],"file":[{"file_id":"7617","file_size":1934830,"date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-24T07:36:36Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"9138977a06fcd6a95976eb4bca875f0c","file_name":"2019_ARCH19_Immler.pdf","relation":"main_file"}],"_id":"7576","language":[{"iso":"eng"}],"page":"41-61"},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"quality_controlled":"1","department":[{"_id":"GaTk"}],"publisher":"IEEE","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.01475"}],"type":"conference","oa_version":"Preprint","date_created":"2020-03-22T23:00:47Z","scopus_import":"1","date_published":"2019-08-01T00:00:00Z","status":"public","publication":"IEEE Information Theory Workshop, ITW 2019","abstract":[{"lang":"eng","text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"external_id":{"arxiv":["1812.01475"],"isi":["000540384500015"]},"title":"A tight upper bound on mutual information","doi":"10.1109/ITW44776.2019.8989292","date_updated":"2025-06-30T13:21:05Z","publication_identifier":{"isbn":["9781538669006"]},"day":"01","ec_funded":1,"year":"2019","related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}]},"conference":{"start_date":"2019-08-25","end_date":"2019-08-28","location":"Visby, Sweden","name":"Information Theory Workshop"},"oa":1,"article_processing_charge":"No","article_number":"8989292","month":"08","author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"citation":{"short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” <i>IEEE Information Theory Workshop, ITW 2019</i>, 8989292, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>.","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in <i>IEEE Information Theory Workshop, ITW 2019</i>, Visby, Sweden, 2019.","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>.","apa":"Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2019). A tight upper bound on mutual information. In <i>IEEE Information Theory Workshop, ITW 2019</i>. Visby, Sweden: IEEE. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>"},"_id":"7606","language":[{"iso":"eng"}]},{"title":"A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering","day":"26","publication_status":"submitted","date_updated":"2020-04-06T10:36:21Z","publisher":"ChemRxiv","year":"2019","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv.11447775.v1"}],"type":"preprint","article_processing_charge":"No","oa":1,"oa_version":"Preprint","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"first_name":"Aleksej","last_name":"Samojlov","full_name":"Samojlov, Aleksej"},{"first_name":"Manfred","last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred"},{"last_name":"Kriechbaum","first_name":"Manfred","full_name":"Kriechbaum, Manfred"},{"full_name":"Amenitsch, Heinz","last_name":"Amenitsch","first_name":"Heinz"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"month":"12","extern":"1","date_created":"2020-04-01T10:10:21Z","citation":{"ieee":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S. A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.” ChemRxiv.","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv, n.d.","mla":"Prehal, Christian, et al. <i>A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering</i>. ChemRxiv.","short":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, (n.d.).","ama":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., &#38; Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. ChemRxiv.","ista":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering."},"page":"50","abstract":[{"lang":"eng","text":"Electrodepositing  insulating  and  insoluble  Li2O2  is  the  key  process  during  discharge  of  aprotic  Li-O2 batteries  and  determines  rate,  capacity,  and  reversibility.  Current  understanding  states  that  the partition  between  surface  adsorbed  and  solvated  LiO2  governs  whether  Li2O2  grows  as  surface  film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We  describe  a  unified  Li2O2  growth  model  that  conclusively  explains  capacity  limitations  across  the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities,   electrode   specific   surface   area   (determining  true   areal   rate)   and   the  concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low   capacity   via   surface   growth.   The   tools   for   these   insights   are   microscopy,   hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with  atomic  to  sub-micron  resolution  to  study  mechanisms  in  complex  electrochemical  systems  and beyond. "}],"date_published":"2019-12-26T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7627","language":[{"iso":"eng"}]},{"article_number":"748-752","month":"10","oa_version":"None","author":[{"full_name":"Rannen-Triki, Amal","first_name":"Amal","last_name":"Rannen-Triki"},{"last_name":"Berman","first_name":"Maxim","full_name":"Berman, Maxim"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blaschko","first_name":"Matthew B.","full_name":"Blaschko, Matthew B."}],"scopus_import":"1","date_created":"2020-04-05T22:00:50Z","citation":{"ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, Seoul, South Korea, 2019.","chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, 748–752, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., &#38; Blaschko, M. B. (2019). Function norms for neural networks. In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. Seoul, South Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752."},"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN."}],"date_published":"2019-10-01T00:00:00Z","status":"public","publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"_id":"7639","department":[{"_id":"VlKo"}],"title":"Function norms for neural networks","doi":"10.1109/ICCVW.2019.00097","isi":1,"external_id":{"isi":["000554591600090"]},"quality_controlled":"1","publication_identifier":{"isbn":["9781728150239"]},"publication_status":"published","day":"01","publisher":"IEEE","date_updated":"2023-09-08T11:19:12Z","conference":{"start_date":"2019-10-27","end_date":"2019-10-28","location":"Seoul, South Korea","name":"ICCVW: International Conference on Computer Vision Workshop"},"year":"2019","type":"conference","article_processing_charge":"No"},{"type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1807.02136","open_access":"1"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}],"project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We propose a new model for detecting visual relationships, such as \"person riding motorcycle\" or \"bottle on table\". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results."}],"status":"public","date_published":"2019-10-01T00:00:00Z","publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","scopus_import":"1","date_created":"2020-04-05T22:00:51Z","oa_version":"Preprint","oa":1,"article_processing_charge":"No","conference":{"end_date":"2019-10-28","start_date":"2019-10-27","name":"ICCVW: International Conference on Computer Vision Workshop","location":"Seoul, South Korea"},"year":"2019","ec_funded":1,"publication_identifier":{"isbn":["9781728150239"]},"day":"01","date_updated":"2023-09-08T11:18:37Z","title":"Detecting visual relationships using box attention","doi":"10.1109/ICCVW.2019.00217","isi":1,"external_id":{"isi":["000554591601098"],"arxiv":["1807.02136"]},"_id":"7640","language":[{"iso":"eng"}],"arxiv":1,"citation":{"apa":"Kolesnikov, A., Kuznetsova, A., Lampert, C., &#38; Ferrari, V. (2019). Detecting visual relationships using box attention. In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. Seoul, South Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">https://doi.org/10.1109/ICCVW.2019.00217</a>","ista":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.","ama":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">10.1109/ICCVW.2019.00217</a>","short":"A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","mla":"Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, 1749–1753, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">10.1109/ICCVW.2019.00217</a>.","ieee":"A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, Seoul, South Korea, 2019.","chicago":"Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">https://doi.org/10.1109/ICCVW.2019.00217</a>."},"article_number":"1749-1753","month":"10","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"},{"first_name":"Alina","last_name":"Kuznetsova","full_name":"Kuznetsova, Alina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}]},{"_id":"7710","intvolume":"        10","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-11-28T00:00:00Z","status":"public","publication":"Nature Communications","abstract":[{"lang":"eng","text":"The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle."}],"date_created":"2020-04-30T10:40:32Z","citation":{"ista":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436.","apa":"Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., &#38; Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13225-y\">https://doi.org/10.1038/s41467-019-13225-y</a>","ama":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13225-y\">10.1038/s41467-019-13225-y</a>","mla":"Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” <i>Nature Communications</i>, vol. 10, 5436, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13225-y\">10.1038/s41467-019-13225-y</a>.","short":"O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019).","chicago":"Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13225-y\">https://doi.org/10.1038/s41467-019-13225-y</a>.","ieee":"O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019."},"extern":"1","article_type":"original","month":"11","article_number":"5436","oa_version":"Published Version","author":[{"first_name":"Olivier","last_name":"Delaneau","full_name":"Delaneau, Olivier"},{"full_name":"Zagury, Jean-François","last_name":"Zagury","first_name":"Jean-François"},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Jonathan L.","last_name":"Marchini","full_name":"Marchini, Jonathan L."},{"full_name":"Dermitzakis, Emmanouil T.","first_name":"Emmanouil T.","last_name":"Dermitzakis"}],"article_processing_charge":"No","oa":1,"volume":10,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-019-13225-y"}],"year":"2019","publisher":"Springer Nature","date_updated":"2021-01-12T08:15:01Z","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","day":"28","quality_controlled":"1","title":"Accurate, scalable and integrative haplotype estimation","doi":"10.1038/s41467-019-13225-y"},{"day":"09","publication_status":"published","publication_identifier":{"issn":["2522-5812"]},"date_updated":"2021-01-12T08:15:01Z","publisher":"Springer Nature","doi":"10.1038/s42255-019-0147-3","title":"Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel","quality_controlled":"1","type":"journal_article","volume":1,"article_processing_charge":"No","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-020-0202-0"}]},"year":"2019","article_type":"original","extern":"1","date_created":"2020-04-30T10:40:56Z","citation":{"ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. <i>Nature Metabolism</i>. 2019;1(12):1226-1242. doi:<a href=\"https://doi.org/10.1038/s42255-019-0147-3\">10.1038/s42255-019-0147-3</a>","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-019-0147-3\">https://doi.org/10.1038/s42255-019-0147-3</a>","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.","ieee":"R. P. J. Bevers <i>et al.</i>, “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” <i>Nature Metabolism</i>, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.","chicago":"Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” <i>Nature Metabolism</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42255-019-0147-3\">https://doi.org/10.1038/s42255-019-0147-3</a>.","mla":"Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” <i>Nature Metabolism</i>, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:<a href=\"https://doi.org/10.1038/s42255-019-0147-3\">10.1038/s42255-019-0147-3</a>.","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242."},"oa_version":"None","author":[{"full_name":"Bevers, Roel P. J.","last_name":"Bevers","first_name":"Roel P. J."},{"full_name":"Litovchenko, Maria","last_name":"Litovchenko","first_name":"Maria"},{"last_name":"Kapopoulou","first_name":"Adamandia","full_name":"Kapopoulou, Adamandia"},{"full_name":"Braman, Virginie S.","last_name":"Braman","first_name":"Virginie S."},{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Auwerx","first_name":"Johan","full_name":"Auwerx, Johan"},{"first_name":"Brian","last_name":"Hollis","full_name":"Hollis, Brian"},{"full_name":"Deplancke, Bart","last_name":"Deplancke","first_name":"Bart"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         1","_id":"7711","language":[{"iso":"eng"}],"page":"1226-1242","abstract":[{"text":"The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies.","lang":"eng"}],"issue":"12","publication":"Nature Metabolism","status":"public","date_published":"2019-12-09T00:00:00Z"},{"publication":"bioRxiv","date_published":"2019-06-14T00:00:00Z","status":"public","page":"20","abstract":[{"lang":"eng","text":"As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures."}],"_id":"7782","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sulc","first_name":"Jonathan","full_name":"Sulc, Jonathan"},{"first_name":"Ninon","last_name":"Mounier","full_name":"Mounier, Ninon"},{"full_name":"Günther, Felix","last_name":"Günther","first_name":"Felix"},{"last_name":"Winkler","first_name":"Thomas","full_name":"Winkler, Thomas"},{"first_name":"Andrew R.","last_name":"Wood","full_name":"Wood, Andrew R."},{"last_name":"Frayling","first_name":"Timothy M.","full_name":"Frayling, Timothy M."},{"full_name":"Heid, Iris M.","first_name":"Iris M.","last_name":"Heid"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Zoltán","last_name":"Kutalik","full_name":"Kutalik, Zoltán"}],"oa_version":"Preprint","month":"06","citation":{"apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .","ama":"Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. <i>bioRxiv</i>. 2019.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019).","mla":"Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2019.","ieee":"J. Sulc <i>et al.</i>, “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2019.","chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2019."},"date_created":"2020-04-30T13:04:26Z","extern":"1","year":"2019","main_file_link":[{"url":"https://doi.org/10.1101/632380 ","open_access":"1"}],"article_processing_charge":"No","oa":1,"type":"preprint","title":"Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank","date_updated":"2021-01-12T08:15:30Z","publisher":"Cold Spring Harbor Laboratory","day":"14","publication_status":"published"},{"_id":"7950","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-03-16T00:00:00Z","status":"public","publication":"arXiv","abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex.  The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete.  We present some partial results:\r\n1.  An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2.  Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3.  Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3.  A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars.  In this version, tokens and  vertices  have  colours,  and  colours  have  weights.   The  goal  is  to  get  every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"date_created":"2020-06-08T12:25:25Z","citation":{"ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. <i>arXiv</i>.","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. <i>arXiv</i>.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981.","ieee":"A. Biniaz <i>et al.</i>, “Token swapping on trees,” <i>arXiv</i>. .","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” <i>ArXiv</i>, n.d.","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” <i>ArXiv</i>, 1903.06981.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.)."},"arxiv":1,"article_number":"1903.06981","month":"03","author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"last_name":"Jain","first_name":"Kshitij","full_name":"Jain, Kshitij"},{"last_name":"Lubiw","first_name":"Anna","full_name":"Lubiw, Anna"},{"first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"full_name":"Miltzow, Tillmann","last_name":"Miltzow","first_name":"Tillmann"},{"last_name":"Mondal","first_name":"Debajyoti","full_name":"Mondal, Debajyoti"},{"full_name":"Naredla, Anurag Murty","last_name":"Naredla","first_name":"Anurag Murty"},{"last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"first_name":"Alexi","last_name":"Turcotte","full_name":"Turcotte, Alexi"}],"oa_version":"Preprint","article_processing_charge":"No","oa":1,"type":"preprint","year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1903.06981","open_access":"1"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"7944","status":"public"},{"id":"12833","relation":"later_version","status":"public"}]},"date_updated":"2024-01-04T12:42:08Z","publication_status":"submitted","day":"16","external_id":{"arxiv":["1903.06981"]},"title":"Token swapping on trees","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}]},{"oa_version":"Published Version","date_created":"2018-12-11T11:44:07Z","scopus_import":"1","date_published":"2019-01-09T00:00:00Z","status":"public","publist_id":"8048","publication":"Journal of Neuroscience","abstract":[{"lang":"eng","text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification."}],"intvolume":"        39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7"}],"pmid":1,"quality_controlled":"1","department":[{"_id":"DaSi"}],"publisher":"Society for Neuroscience","publication_status":"published","volume":39,"type":"journal_article","month":"01","file_date_updated":"2020-10-02T09:33:28Z","file":[{"file_id":"8596","success":1,"file_size":9455414,"date_created":"2020-10-02T09:33:28Z","date_updated":"2020-10-02T09:33:28Z","access_level":"open_access","content_type":"application/pdf","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","creator":"dernst","relation":"main_file","file_name":"2019_JournNeuroscience_Trebuchet.pdf"}],"author":[{"last_name":"Trébuchet","first_name":"Guillaume","full_name":"Trébuchet, Guillaume"},{"last_name":"Cattenoz","first_name":"Pierre B","full_name":"Cattenoz, Pierre B"},{"full_name":"Zsámboki, János","last_name":"Zsámboki","first_name":"János"},{"first_name":"David","last_name":"Mazaud","full_name":"Mazaud, David"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus"},{"first_name":"Manolis","last_name":"Fanto","full_name":"Fanto, Manolis"},{"last_name":"Giangrande","first_name":"Angela","full_name":"Giangrande, Angela"}],"citation":{"short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” <i>Journal of Neuroscience</i>, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">10.1523/JNEUROSCI.1059-18.2018</a>.","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2019. <a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">https://doi.org/10.1523/JNEUROSCI.1059-18.2018</a>.","ieee":"G. Trébuchet <i>et al.</i>, “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” <i>Journal of Neuroscience</i>, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255.","apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., &#38; Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">https://doi.org/10.1523/JNEUROSCI.1059-18.2018</a>","ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. <i>Journal of Neuroscience</i>. 2019;39(2):238-255. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1059-18.2018\">10.1523/JNEUROSCI.1059-18.2018</a>"},"ddc":["570"],"article_type":"original","issue":"2","page":"238-255","acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","_id":"8","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000455189900006"],"pmid":["30504274"]},"title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","doi":"10.1523/JNEUROSCI.1059-18.2018","date_updated":"2023-09-19T10:10:55Z","day":"09","ec_funded":1,"year":"2019","has_accepted_license":"1","oa":1,"article_processing_charge":"No"},{"has_accepted_license":"1","year":"2019","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","oa":1,"title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","doi":"10.1007/s00220-018-3239-0","isi":1,"external_id":{"isi":["000467796800007"]},"day":"01","date_updated":"2023-08-24T14:27:51Z","page":"723-776","issue":"2","_id":"80","language":[{"iso":"eng"}],"month":"06","file_date_updated":"2020-07-14T12:48:07Z","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2018_CommunMathPhys_Deuchert.pdf","creator":"dernst","checksum":"c7e9880b43ac726712c1365e9f2f73a6","file_size":893902,"file_id":"5688","access_level":"open_access","date_updated":"2020-07-14T12:48:07Z","date_created":"2018-12-17T10:34:06Z"}],"author":[{"last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"},{"last_name":"Yngvason","first_name":"Jakob","full_name":"Yngvason, Jakob"}],"article_type":"original","citation":{"ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. <i>Communications in Mathematical Physics</i>. 2019;368(2):723-776. doi:<a href=\"https://doi.org/10.1007/s00220-018-3239-0\">10.1007/s00220-018-3239-0</a>","ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776.","apa":"Deuchert, A., Seiringer, R., &#38; Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-018-3239-0\">https://doi.org/10.1007/s00220-018-3239-0</a>","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” <i>Communications in Mathematical Physics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00220-018-3239-0\">https://doi.org/10.1007/s00220-018-3239-0</a>.","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” <i>Communications in Mathematical Physics</i>, vol. 368, no. 2. Springer, pp. 723–776, 2019.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776.","mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” <i>Communications in Mathematical Physics</i>, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:<a href=\"https://doi.org/10.1007/s00220-018-3239-0\">10.1007/s00220-018-3239-0</a>."},"ddc":["530"],"volume":368,"type":"journal_article","department":[{"_id":"RoSe"}],"project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"quality_controlled":"1","publication_status":"published","publisher":"Springer","abstract":[{"text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.","lang":"eng"}],"status":"public","date_published":"2019-06-01T00:00:00Z","publication":"Communications in Mathematical Physics","publist_id":"7974","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       368","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","scopus_import":"1","date_created":"2018-12-11T11:44:31Z"},{"publisher":"Public Library of Science","publication_status":"published","pmid":1,"quality_controlled":"1","volume":15,"type":"journal_article","date_created":"2020-06-25T12:50:39Z","extern":"1","oa_version":"Published Version","intvolume":"        15","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","date_published":"2019-07-11T00:00:00Z","publication":"PLOS Computational Biology","date_updated":"2021-01-12T08:16:31Z","publication_identifier":{"issn":["1553-7358"]},"day":"11","external_id":{"pmid":["31295253"]},"title":"Think: Theory for Africa","doi":"10.1371/journal.pcbi.1007049","article_processing_charge":"No","oa":1,"year":"2019","has_accepted_license":"1","citation":{"short":"C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019).","mla":"Currin, Christopher B., et al. “Think: Theory for Africa.” <i>PLOS Computational Biology</i>, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007049\">10.1371/journal.pcbi.1007049</a>.","chicago":"Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” <i>PLOS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007049\">https://doi.org/10.1371/journal.pcbi.1007049</a>.","ieee":"C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” <i>PLOS Computational Biology</i>, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.","apa":"Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., &#38; Raimondo, J. V. (2019). Think: Theory for Africa. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007049\">https://doi.org/10.1371/journal.pcbi.1007049</a>","ama":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. <i>PLOS Computational Biology</i>. 2019;15(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007049\">10.1371/journal.pcbi.1007049</a>"},"ddc":["570"],"article_type":"original","month":"07","file_date_updated":"2020-07-14T12:48:08Z","article_number":"e1007049","file":[{"creator":"cziletti","checksum":"723bdfb6ee5c747cbbb32baf01d17fad","file_name":"2019_PlosCompBio_Currin.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2020-07-02T12:22:57Z","date_updated":"2020-07-14T12:48:08Z","access_level":"open_access","file_id":"8079","file_size":773969}],"author":[{"full_name":"Currin, Christopher B.","first_name":"Christopher B.","last_name":"Currin"},{"first_name":"Phumlani N.","last_name":"Khoza","full_name":"Khoza, Phumlani N."},{"full_name":"Antrobus, Alexander D.","first_name":"Alexander D.","last_name":"Antrobus"},{"full_name":"Latham, Peter E.","last_name":"Latham","first_name":"Peter E."},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Raimondo","first_name":"Joseph V.","full_name":"Raimondo, Joseph V."}],"language":[{"iso":"eng"}],"_id":"8013","issue":"7"}]