[{"main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"type":"journal_article","isi":1,"month":"06","intvolume":"       115","issue":"26","ec_funded":1,"page":"6864-6869","citation":{"chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. 2018;115(26):6864-6869. doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ieee":"M. Abbas <i>et al.</i>, “Auxin methylation is required for differential growth in Arabidopsis,” <i>PNAS</i>, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018."},"quality_controlled":"1","publication_status":"published","publist_id":"7710","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"publication":"PNAS","scopus_import":"1","publisher":"National Academy of Sciences","title":"Auxin methylation is required for differential growth in Arabidopsis","article_processing_charge":"No","_id":"203","date_updated":"2025-05-07T11:12:32Z","year":"2018","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"oa":1,"author":[{"id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abbas","full_name":"Abbas, Mohamad","first_name":"Mohamad"},{"last_name":"Hernández","full_name":"Hernández, García J","first_name":"García J"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"last_name":"Samodelov","full_name":"Samodelov, Sophia L","first_name":"Sophia L"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hammes","first_name":"Ulrich Z","full_name":"Hammes, Ulrich Z"},{"last_name":"Zurbriggen","full_name":"Zurbriggen, Matias D","first_name":"Matias D"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"full_name":"Alabadí, David","first_name":"David","last_name":"Alabadí"}],"status":"public","oa_version":"None","volume":115,"date_created":"2018-12-11T11:45:11Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1073/pnas.1806565115","external_id":{"isi":["000436245000096"]},"date_published":"2018-06-26T00:00:00Z","day":"26"},{"day":"30","date_published":"2018-07-30T00:00:00Z","external_id":{"isi":["000448185000055"]},"doi":"10.1145/3197517.3201336","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:48Z","volume":37,"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"status":"public","author":[{"first_name":"Stefan","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke"},{"first_name":"Tomas","full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan"},{"first_name":"Matthias","full_name":"Mueller Fischer, Matthias","last_name":"Mueller Fischer"},{"last_name":"Chentanez","first_name":"Nuttapong","full_name":"Chentanez, Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2018","has_accepted_license":"1","date_updated":"2024-02-28T13:58:51Z","_id":"134","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","description":"News on IST Homepage"}]},"article_processing_charge":"No","title":"Water surface wavelets","publisher":"ACM","scopus_import":"1","publication":"ACM Transactions on Graphics","file_date_updated":"2020-07-14T12:44:45Z","file":[{"content_type":"application/pdf","checksum":"db75ebabe2ec432bf41389e614d6ef62","access_level":"open_access","creator":"dernst","file_id":"5744","relation":"main_file","date_created":"2018-12-18T09:59:23Z","file_size":22185016,"date_updated":"2020-07-14T12:44:45Z","file_name":"2018_ACM_Jeschke.pdf"}],"abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"7789","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_status":"published","quality_controlled":"1","alternative_title":["SIGGRAPH"],"citation":{"ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. <i>ACM Transactions on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., &#38; Wojtan, C. (2018). Water surface wavelets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4. ACM, 2018.","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4, 94, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018)."},"acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"issue":"4","intvolume":"        37","article_number":"94","isi":1,"month":"07","ddc":["000"],"type":"journal_article"},{"article_processing_charge":"No","title":"Extended narrow band FLIP for liquid simulations","_id":"135","date_updated":"2023-09-11T14:00:26Z","has_accepted_license":"1","year":"2018","project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"publication_identifier":{"issn":["0167-7055"]},"oa":1,"status":"public","author":[{"last_name":"Sato","first_name":"Takahiro","full_name":"Sato, Takahiro"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"last_name":"Igarashi","full_name":"Igarashi, Takeo","first_name":"Takeo"},{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"}],"oa_version":"Submitted Version","volume":37,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:49Z","doi":"10.1111/cgf.13351","external_id":{"isi":["000434085600016"]},"date_published":"2018-05-22T00:00:00Z","day":"22","type":"journal_article","ddc":["006"],"isi":1,"month":"05","intvolume":"        37","issue":"2","ec_funded":1,"page":"169 - 177","citation":{"short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2018). Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. 2018;37(2):169-177. doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>"},"alternative_title":["Eurographics"],"quality_controlled":"1","publication_status":"published","article_type":"original","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"publication":"Computer Graphics Forum","file_date_updated":"2020-10-08T08:38:23Z","file":[{"creator":"wojtan","access_level":"open_access","content_type":"application/pdf","checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627","relation":"main_file","file_name":"exnbflip.pdf","date_updated":"2020-10-08T08:38:23Z","success":1,"file_size":54309947,"date_created":"2020-10-08T08:38:23Z"}],"scopus_import":"1","publisher":"Wiley"},{"year":"2018","oa":1,"title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","article_processing_charge":"No","_id":"136","date_updated":"2023-10-10T13:29:10Z","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"date_published":"2018-08-13T00:00:00Z","day":"13","author":[{"full_name":"Suri, Balachandra","first_name":"Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tithof","full_name":"Tithof, Jeffrey","first_name":"Jeffrey"},{"full_name":"Grigoriev, Roman","first_name":"Roman","last_name":"Grigoriev"},{"last_name":"Schatz","first_name":"Michael","full_name":"Schatz, Michael"}],"status":"public","oa_version":"Submitted Version","volume":98,"date_created":"2018-12-11T11:44:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevE.98.023105","isi":1,"month":"08","intvolume":"        98","issue":"2","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"publication":"Physical Review E","scopus_import":"1","publisher":"American Physical Society","citation":{"ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 98, no. 2. American Physical Society, 2018.","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 98, no. 2, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>.","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. 2018;98(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>","apa":"Suri, B., Tithof, J., Grigoriev, R., &#38; Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>."},"quality_controlled":"1","publication_status":"published"},{"abstract":[{"text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"7786","department":[{"_id":"HaJa"}],"publisher":"Nature Publishing Group","scopus_import":"1","publication":"Nature Chemical Biology","citation":{"apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. 2018;14(9):861-869. doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ieee":"W. Zhang <i>et al.</i>, “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” <i>Nature Chemical Biology</i>, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018."},"quality_controlled":"1","article_type":"original","publication_status":"published","intvolume":"        14","isi":1,"month":"07","page":"861 - 869","issue":"9","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"type":"journal_article","external_id":{"isi":["000442174500013"],"pmid":["30061718 "]},"day":"30","date_published":"2018-07-30T00:00:00Z","oa_version":"Submitted Version","author":[{"last_name":"Zhang","full_name":"Zhang, William","first_name":"William"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"first_name":"Andreas","full_name":"Wulff, Andreas","last_name":"Wulff"},{"last_name":"Vongsouthi","first_name":"Vanessa","full_name":"Vongsouthi, Vanessa"},{"last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Gulakova, Polina","first_name":"Polina","last_name":"Gulakova"},{"full_name":"Minge, Daniel","first_name":"Daniel","last_name":"Minge"},{"last_name":"Breithausen","full_name":"Breithausen, Björn","first_name":"Björn"},{"last_name":"Schoch","first_name":"Susanne","full_name":"Schoch, Susanne"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"}],"status":"public","doi":"10.1038/s41589-018-0108-2","pmid":1,"volume":14,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:49Z","year":"2018","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"}],"oa":1,"article_processing_charge":"No","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","_id":"137","date_updated":"2023-09-13T08:58:05Z"},{"author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"first_name":"Pierre","full_name":"Gagnaire, Pierre","last_name":"Gagnaire"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"last_name":"Faivre","full_name":"Faivre, Nicolas","first_name":"Nicolas"},{"last_name":"Welch","full_name":"Welch, John","first_name":"John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:44:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2018,"doi":"10.7717/peerj.5198","external_id":{"isi":["000440484800002"]},"date_published":"2018-07-30T00:00:00Z","day":"30","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","article_processing_charge":"No","date_updated":"2023-10-17T12:25:28Z","_id":"139","has_accepted_license":"1","year":"2018","oa":1,"quality_controlled":"1","citation":{"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. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","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.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","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.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018)."},"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"7784","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","publication":"PeerJ","file_date_updated":"2020-07-14T12:44:48Z","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"7d55ae22598a1c70759cd671600cff53","file_id":"5739","relation":"main_file","date_updated":"2020-07-14T12:44:48Z","file_name":"2018_PeerJ_Fraisse.pdf","date_created":"2018-12-18T09:42:11Z","file_size":1480792}],"publisher":"PeerJ","ddc":["576"],"type":"journal_article","month":"07","isi":1,"intvolume":"      2018","article_number":"30083438","issue":"7"},{"year":"2018","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"eissn":["1422-0067"]},"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","article_processing_charge":"No","_id":"14","date_updated":"2023-09-18T08:09:32Z","external_id":{"isi":["000451528500282"]},"day":"12","date_published":"2018-11-12T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Hille, Sander","first_name":"Sander","last_name":"Hille"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","full_name":"Akhmanova, Maria","first_name":"Maria","orcid":"0000-0003-1522-3162"},{"last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Johnson, Alexander J","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.3390/ijms19113566","volume":19,"date_created":"2018-12-11T11:44:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        19","isi":1,"month":"11","ec_funded":1,"issue":"11","type":"journal_article","ddc":["580"],"abstract":[{"text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta.","lang":"eng"}],"department":[{"_id":"DaSi"},{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publist_id":"8042","publisher":"MDPI","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","file_id":"5719","relation":"main_file","file_name":"2018_IJMS_Hille.pdf","date_updated":"2020-07-14T12:44:50Z","date_created":"2018-12-17T16:04:11Z","file_size":2200593}],"scopus_import":"1","publication":"International Journal of Molecular Sciences","file_date_updated":"2020-07-14T12:44:50Z","citation":{"chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>.","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., &#38; Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. 2018;19(11). doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>.","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11. MDPI, 2018.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11)."},"quality_controlled":"1","article_type":"original","publication_status":"published"},{"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publist_id":"7783","abstract":[{"text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools.","lang":"eng"}],"scopus_import":"1","file":[{"date_updated":"2020-07-14T12:44:50Z","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","date_created":"2018-12-12T10:17:53Z","file_size":563710,"relation":"main_file","file_id":"5310","access_level":"open_access","creator":"system","checksum":"6dca832f575d6b3f0ea9dff56f579142","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:44:50Z","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":"1","citation":{"chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>.","apa":"Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","mla":"Frehse, Goran, et al. <i>Space-Time Interpolants</i>. Vol. 10981, Springer, 2018, pp. 468–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>.","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486."},"publication_status":"published","month":"07","isi":1,"pubrep_id":"1010","intvolume":"     10981","page":"468 - 486","ddc":["005"],"type":"conference","external_id":{"isi":["000491481600025"]},"date_published":"2018-07-18T00:00:00Z","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","full_name":"Giacobbe, Mirco"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:50Z","volume":10981,"doi":"10.1007/978-3-319-96145-3_25","has_accepted_license":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"year":"2018","publication_identifier":{"issn":["03029743"]},"oa":1,"title":"Space-time interpolants","article_processing_charge":"No","related_material":{"record":[{"status":"public","id":"6894","relation":"dissertation_contains"}]},"conference":{"start_date":"2018-07-14","end_date":"2018-07-17","location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification"},"date_updated":"2023-09-19T09:30:43Z","_id":"140"},{"volume":10982,"date_created":"2018-12-11T11:44:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1007/978-3-319-96142-2_13","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"},{"first_name":"Simin","full_name":"Oraee, Simin","last_name":"Oraee"},{"last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor"}],"status":"public","oa_version":"Published Version","date_published":"2018-07-18T00:00:00Z","day":"18","external_id":{"isi":["000491469700013"]},"related_material":{"record":[{"status":"public","id":"10199","relation":"dissertation_contains"}]},"conference":{"location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification","start_date":"2018-07-14","end_date":"2018-07-17"},"_id":"141","date_updated":"2025-07-14T09:10:15Z","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","article_processing_charge":"No","oa":1,"has_accepted_license":"1","year":"2018","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","publication_status":"published","citation":{"apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., &#38; Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>","mla":"Chatterjee, Krishnendu, et al. <i>Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives</i>. Vol. 10982, Springer, 2018, pp. 178–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197."},"quality_controlled":"1","alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:44:53Z","file":[{"date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Chatterjee.pdf","file_size":675606,"date_created":"2018-12-18T08:52:38Z","relation":"main_file","file_id":"5737","access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc"}],"scopus_import":"1","publisher":"Springer","department":[{"_id":"KrCh"}],"publist_id":"7782","language":[{"iso":"eng"}],"abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"type":"conference","ddc":["000"],"ec_funded":1,"page":"178-197","isi":1,"month":"07","intvolume":"     10982"},{"abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1806.02199"]},"day":"06","publication":"International Conference on Learning Representations","date_published":"2018-06-06T00:00:00Z","oa_version":"Preprint","citation":{"ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: <i>International Conference on Learning Representations</i>. ; 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., &#38; Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In <i>International Conference on Learning Representations</i>. New Orleans, LA, United States.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In <i>International Conference on Learning Representations</i>, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in <i>International Conference on Learning Representations</i>, New Orleans, LA, United States, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” <i>International Conference on Learning Representations</i>, 2018."},"extern":"1","author":[{"full_name":"Fortuin, Vincent","first_name":"Vincent","last_name":"Fortuin"},{"last_name":"Hüser","full_name":"Hüser, Matthias","first_name":"Matthias"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"last_name":"Strathmann","first_name":"Heiko","full_name":"Strathmann, Heiko"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"quality_controlled":"1","status":"public","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:12:48Z","year":"2018","month":"06","oa":1,"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","article_processing_charge":"No","type":"conference","_id":"14198","date_updated":"2023-09-13T06:35:12Z","conference":{"end_date":"2019-05-09","start_date":"2019-05-06","location":"New Orleans, LA, United States","name":"ICLR: International Conference on Learning Representations"}},{"abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"7781","language":[{"iso":"eng"}],"publisher":"Springer","scopus_import":"1","file":[{"relation":"main_file","date_created":"2018-12-17T15:57:06Z","file_size":5591566,"date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Kong.pdf","checksum":"fd95e8026deacef3dc752a733bb9355f","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5718"}],"file_date_updated":"2020-07-14T12:44:53Z","alternative_title":["LNCS"],"quality_controlled":"1","citation":{"mla":"Kong, Hui, et al. <i>Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes</i>. Vol. 10981, Springer, 2018, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","apa":"Kong, H., Bartocci, E., &#38; Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>"},"publication_status":"published","intvolume":"     10981","month":"07","isi":1,"page":"449 - 467","ddc":["000"],"type":"conference","external_id":{"isi":["000491481600024"]},"day":"18","date_published":"2018-07-18T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"doi":"10.1007/978-3-319-96145-3_24","date_created":"2018-12-11T11:44:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10981,"acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","year":"2018","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"article_processing_charge":"No","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","date_updated":"2023-09-15T12:12:08Z","_id":"142","conference":{"end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification","location":"Oxford, United Kingdom"}},{"year":"2018","oa":1,"title":"Boosting variational inference: An optimization perspective","article_processing_charge":"No","_id":"14201","date_updated":"2023-09-13T07:52:40Z","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote","end_date":"2018-04-11","start_date":"2018-04-09"},"external_id":{"arxiv":["1708.01733"]},"day":"15","date_published":"2018-04-15T00:00:00Z","oa_version":"Preprint","extern":"1","author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"last_name":"Ghosh","first_name":"Joydeep","full_name":"Ghosh, Joydeep"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"status":"public","volume":84,"date_created":"2023-08-22T14:15:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        84","month":"04","page":"464-472","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"type":"conference","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publisher":"ML Research Press","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","scopus_import":"1","citation":{"ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, vol. 84, ML Research Press, 2018, pp. 464–72.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>. Vol 84. ML Research Press; 2018:464-472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, 84:464–72. ML Research Press, 2018.","apa":"Locatello, F., Khanna, R., Ghosh, J., &#38; Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i> (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press."},"alternative_title":["PMLR"],"quality_controlled":"1","publication_status":"published"},{"abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems Foundation","publication":"Advances in Neural Information Processing Systems","scopus_import":"1","quality_controlled":"1","citation":{"ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: <i>Advances in Neural Information Processing Systems</i>. Vol 31. Neural Information Processing Systems Foundation; 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., &#38; Rätsch, G. (2018). Boosting black box variational inference. In <i>Advances in Neural Information Processing Systems</i> (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 31. Neural Information Processing Systems Foundation, 2018.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 31.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” <i>Advances in Neural Information Processing Systems</i>, vol. 31, Neural Information Processing Systems Foundation, 2018.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018."},"publication_status":"published","intvolume":"        31","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1806.02185","open_access":"1"}],"arxiv":1,"type":"conference","external_id":{"arxiv":["1806.02185"]},"day":"06","date_published":"2018-06-06T00:00:00Z","oa_version":"Preprint","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"last_name":"Valera","first_name":"Isabel","full_name":"Valera, Isabel"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"status":"public","extern":"1","date_created":"2023-08-22T14:15:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":31,"year":"2018","oa":1,"publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"title":"Boosting black box variational inference","article_processing_charge":"No","date_updated":"2023-09-13T07:38:24Z","_id":"14202","conference":{"end_date":"2018-12-08","start_date":"2018-12-03","location":"Montreal, Canada","name":"NeurIPS: Neural Information Processing Systems"}},{"alternative_title":["PMLR"],"quality_controlled":"1","citation":{"ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:5727-5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., &#38; Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:5727–36. ML Research Press, 2018.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 5727–36."},"publication_status":"published","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"abstract":[{"text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework.","lang":"eng"}],"publication":"Proceedings of the 35th International Conference on Machine Learning","publisher":"ML Research Press","main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}],"arxiv":1,"type":"conference","month":"07","intvolume":"        80","page":"5727-5736","author":[{"first_name":"Alp","full_name":"Yurtsever, Alp","last_name":"Yurtsever"},{"first_name":"Olivier","full_name":"Fercoq, Olivier","last_name":"Fercoq"},{"first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Cevher","full_name":"Cevher, Volkan","first_name":"Volkan"}],"status":"public","extern":"1","oa_version":"Preprint","date_created":"2023-08-22T14:16:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":80,"external_id":{"arxiv":["1804.08544"]},"date_published":"2018-07-15T00:00:00Z","day":"15","article_processing_charge":"No","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","conference":{"end_date":"2018-07-15","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning","location":"Stockholm, Sweden"},"date_updated":"2023-09-13T08:13:39Z","_id":"14203","year":"2018","oa":1},{"publisher":"ML Research Press","scopus_import":"1","publication":"Proceedings of the 35th International Conference on Machine Learning","abstract":[{"text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"publication_status":"published","alternative_title":["PMLR"],"quality_controlled":"1","citation":{"ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","ieee":"F. Locatello <i>et al.</i>, “On matching pursuit and coordinate descent,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, 2018, vol. 80, pp. 3198–3207.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 3198–207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:3198-3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., &#38; Jaggi, M. (2018). On matching pursuit and coordinate descent. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 3198–3207). ML Research Press.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:3198–3207. ML Research Press, 2018."},"page":"3198-3207","intvolume":"        80","month":"07","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"arxiv":1,"day":"01","date_published":"2018-07-01T00:00:00Z","external_id":{"arxiv":["1803.09539"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:16:25Z","volume":80,"oa_version":"Preprint","author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Raj","first_name":"Anant","full_name":"Raj, Anant"},{"full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth","last_name":"Karimireddy"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Sebastian U.","full_name":"Stich, Sebastian U.","last_name":"Stich"},{"first_name":"Martin","full_name":"Jaggi, Martin","last_name":"Jaggi"}],"status":"public","extern":"1","oa":1,"year":"2018","date_updated":"2023-09-13T08:19:05Z","_id":"14204","title":"On matching pursuit and coordinate descent","article_processing_charge":"No"},{"month":"05","year":"2018","oa":1,"title":"Clustering meets implicit generative models","article_processing_charge":"No","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11130"}],"conference":{"name":"International Conference on Machine Learning","location":"Vancouver, Canada","start_date":"2018-04-30","end_date":"2018-05-03"},"type":"conference","_id":"14224","date_updated":"2023-09-13T09:08:24Z","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"external_id":{"arxiv":["1804.11130"]},"abstract":[{"text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples.","lang":"eng"}],"publication":"6th International Conference on Learning Representations","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","day":"01","citation":{"ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In <i>6th International Conference on Learning Representations</i>, 2018.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., &#38; Scholkopf, B. (2018). Clustering meets implicit generative models. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” <i>6th International Conference on Learning Representations</i>, 2018."},"extern":"1","status":"public","quality_controlled":"1","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco"},{"first_name":"Damien","full_name":"Vincent, Damien","last_name":"Vincent"},{"full_name":"Tolstikhin, Ilya","first_name":"Ilya","last_name":"Tolstikhin"},{"last_name":"Ratsch","full_name":"Ratsch, Gunnar","first_name":"Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"last_name":"Scholkopf","first_name":"Bernhard","full_name":"Scholkopf, Bernhard"}],"oa_version":"Preprint","date_created":"2023-08-22T14:25:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1804.10985","open_access":"1"}],"page":"185 - 194","ec_funded":1,"isi":1,"month":"07","publication_status":"published","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"quality_controlled":"1","citation":{"mla":"Brázdil, Tomáš, et al. <i>Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS</i>. Vol. F138033, IEEE, 2018, pp. 185–94, doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>.","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., &#38; Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>"},"scopus_import":"1","publisher":"IEEE","department":[{"_id":"KrCh"}],"publist_id":"7780","language":[{"iso":"eng"}],"abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"conference":{"name":"LICS: Logic in Computer Science","location":"Oxford, United Kingdom","end_date":"2018-07-12","start_date":"2018-07-09"},"date_updated":"2025-06-02T08:53:48Z","_id":"143","article_processing_charge":"No","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"oa":1,"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"year":"2018","date_created":"2018-12-11T11:44:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":"F138033","doi":"10.1145/3209108.3209191","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Novotny, Petr"},{"full_name":"Velan, Dominik","first_name":"Dominik","last_name":"Velan"},{"first_name":"Florian","full_name":"Zuleger, Florian","last_name":"Zuleger"}],"status":"public","oa_version":"Preprint","date_published":"2018-07-09T00:00:00Z","day":"09","external_id":{"isi":["000545262800020"]}},{"author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Vincent, Damien","first_name":"Damien","last_name":"Vincent"},{"last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya","first_name":"Ilya"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"}],"status":"public","extern":"1","citation":{"mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>.","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>"},"oa_version":"Preprint","publication_status":"submitted","date_created":"2023-09-13T12:20:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/arXiv.1804.11130","external_id":{"arxiv":["1804.11130"]},"language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"abstract":[{"text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples.","lang":"eng"}],"date_published":"2018-04-30T00:00:00Z","publication":"arXiv","day":"30","title":"Competitive training of mixtures of independent deep generative models","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1804.11130"}],"arxiv":1,"date_updated":"2023-09-13T12:23:03Z","_id":"14327","type":"preprint","month":"04","year":"2018","article_number":"1804.11130","oa":1},{"volume":"Part F138033","date_created":"2018-12-11T11:44:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","doi":"10.1145/3209108.3209194","citation":{"ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>.","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>"},"quality_controlled":"1","author":[{"full_name":"Ferrere, Thomas","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Ege","full_name":"Saraç, Ege","last_name":"Saraç"}],"status":"public","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"oa_version":"None","scopus_import":"1","date_published":"2018-07-09T00:00:00Z","publisher":"IEEE","day":"09","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publist_id":"7779","external_id":{"isi":["000545262800041"]},"abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"conference":{"name":"LICS: Logic in Computer Science","location":"Oxford, UK","start_date":"2018-07-09","end_date":"2018-07-12"},"type":"conference","_id":"144","date_updated":"2023-09-08T11:49:13Z","article_processing_charge":"No","title":"A theory of register monitors","page":"394 - 403","isi":1,"month":"07","year":"2018"},{"day":"01","date_published":"2018-08-01T00:00:00Z","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"doi":"10.15252/embj.201798044","pmid":1,"volume":37,"date_created":"2018-12-11T11:44:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","author":[{"full_name":"Truckenbrodt, Sven M","first_name":"Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Viplav, Abhiyan","first_name":"Abhiyan","last_name":"Viplav"},{"last_name":"Jähne","full_name":"Jähne, Sebsatian","first_name":"Sebsatian"},{"full_name":"Vogts, Angela","first_name":"Angela","last_name":"Vogts"},{"first_name":"Annette","full_name":"Denker, Annette","last_name":"Denker"},{"full_name":"Wildhagen, Hanna","first_name":"Hanna","last_name":"Wildhagen"},{"last_name":"Fornasiero","full_name":"Fornasiero, Eugenio","first_name":"Eugenio"},{"last_name":"Rizzoli","full_name":"Rizzoli, Silvio","first_name":"Silvio"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa":1,"publication_identifier":{"issn":["0261-4189"]},"year":"2018","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","has_accepted_license":"1","_id":"145","date_updated":"2023-09-13T09:02:48Z","article_processing_charge":"No","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","publisher":"Wiley","file":[{"date_created":"2018-12-17T14:17:29Z","file_size":2846470,"file_name":"2018_EMBO_Truckenbrodt.pdf","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","file_id":"5710","content_type":"application/pdf","checksum":"a540feb6c9af6aefc78de531461a8835","creator":"dernst","access_level":"open_access"}],"scopus_import":"1","publication":"The EMBO Journal","file_date_updated":"2020-07-14T12:44:56Z","abstract":[{"lang":"eng","text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins."}],"department":[{"_id":"JoDa"}],"language":[{"iso":"eng"}],"publist_id":"7778","article_type":"original","publication_status":"published","citation":{"chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018."},"quality_controlled":"1","issue":"15","article_number":"e98044","intvolume":"        37","month":"08","isi":1,"type":"journal_article","ddc":["570"]}]