[{"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"}],"volume":2018,"oa_version":"Published Version","day":"30","external_id":{"isi":["000440484800002"]},"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"07","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2023-10-17T12:25:28Z","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","isi":1,"article_number":"30083438","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>.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","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.","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>.","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."},"date_published":"2018-07-30T00:00:00Z","year":"2018","publication_status":"published","doi":"10.7717/peerj.5198","publisher":"PeerJ","article_processing_charge":"No","file":[{"content_type":"application/pdf","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","creator":"dernst","file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z","relation":"main_file","file_size":1480792,"access_level":"open_access"}],"ddc":["576"],"intvolume":"      2018","publist_id":"7784","status":"public","date_created":"2018-12-11T11:44:50Z","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"PeerJ","file_date_updated":"2020-07-14T12:44:48Z","issue":"7","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"last_name":"Gagnaire","full_name":"Gagnaire, Pierre","first_name":"Pierre"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"first_name":"Nicolas","last_name":"Faivre","full_name":"Faivre, Nicolas"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"oa":1,"_id":"139"},{"month":"11","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"date_updated":"2025-04-14T07:45:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","citation":{"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>","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","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>.","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>","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).","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."},"date_published":"2018-11-12T00:00:00Z","year":"2018","doi":"10.3390/ijms19113566","article_processing_charge":"No","publication_identifier":{"eissn":["1422-0067"]},"publisher":"MDPI","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","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."}],"ec_funded":1,"day":"12","volume":19,"oa_version":"Published Version","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"isi":["000451528500282"]},"issue":"11","file_date_updated":"2020-07-14T12:44:50Z","type":"journal_article","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.","author":[{"last_name":"Hille","full_name":"Hille, Sander","first_name":"Sander"},{"orcid":"0000-0003-1522-3162","first_name":"Maria","last_name":"Akhmanova","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","orcid":"0000-0003-0619-7783"},{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"_id":"14","ddc":["580"],"file":[{"file_name":"2018_IJMS_Hille.pdf","date_updated":"2020-07-14T12:44:50Z","content_type":"application/pdf","creator":"dernst","file_id":"5719","date_created":"2018-12-17T16:04:11Z","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","access_level":"open_access","file_size":2200593,"relation":"main_file"}],"publist_id":"8042","intvolume":"        19","date_created":"2018-12-11T11:44:09Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"International Journal of Molecular Sciences","has_accepted_license":"1"},{"quality_controlled":"1","external_id":{"arxiv":["1806.02199"]},"language":[{"iso":"eng"}],"publication":"International Conference on Learning Representations","oa_version":"Preprint","day":"06","date_created":"2023-08-22T14:12:48Z","status":"public","conference":{"end_date":"2019-05-09","name":"ICLR: International Conference on Learning Representations","start_date":"2019-05-06","location":"New Orleans, LA, United States"},"main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","_id":"14198","arxiv":1,"article_processing_charge":"No","citation":{"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.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","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.","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.","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.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” <i>International Conference on Learning Representations</i>, 2018.","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."},"oa":1,"date_published":"2018-06-06T00:00:00Z","year":"2018","extern":"1","title":"SOM-VAE: Interpretable discrete representation learning on time series","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vincent","full_name":"Fortuin, Vincent","last_name":"Fortuin"},{"full_name":"Hüser, Matthias","last_name":"Hüser","first_name":"Matthias"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Strathmann","full_name":"Strathmann, Heiko","first_name":"Heiko"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"department":[{"_id":"FrLo"}],"month":"06","date_updated":"2023-09-13T06:35:12Z"},{"alternative_title":["LNCS"],"external_id":{"isi":["000491481600024"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"oa_version":"Published Version","day":"18","volume":10981,"conference":{"start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"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"}],"publisher":"Springer","article_processing_charge":"No","doi":"10.1007/978-3-319-96145-3_24","publication_status":"published","date_published":"2018-07-18T00:00:00Z","year":"2018","citation":{"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>","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","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>","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.","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>.","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."},"isi":1,"title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","date_updated":"2025-04-15T06:25:58Z","department":[{"_id":"ToHe"}],"month":"07","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","scopus_import":"1","date_created":"2018-12-11T11:44:51Z","publist_id":"7781","page":"449 - 467","intvolume":"     10981","ddc":["000"],"file":[{"date_created":"2018-12-17T15:57:06Z","checksum":"fd95e8026deacef3dc752a733bb9355f","access_level":"open_access","file_size":5591566,"relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Kong.pdf","content_type":"application/pdf","creator":"dernst","file_id":"5718"}],"_id":"142","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","author":[{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","orcid":"0000-0002-3066-6941"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"type":"conference","file_date_updated":"2020-07-14T12:44:53Z"},{"publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2023-08-22T14:15:20Z","status":"public","intvolume":"        84","page":"464-472","_id":"14201","arxiv":1,"oa":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"first_name":"Joydeep","last_name":"Ghosh","full_name":"Ghosh, Joydeep"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"type":"conference","quality_controlled":"1","external_id":{"arxiv":["1708.01733"]},"alternative_title":["PMLR"],"oa_version":"Preprint","volume":84,"day":"15","conference":{"end_date":"2018-04-11","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2018-04-09","location":"Playa Blanca, Lanzarote"},"abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"publication_status":"published","publisher":"ML Research Press","article_processing_charge":"No","date_published":"2018-04-15T00:00:00Z","year":"2018","citation":{"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.","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.","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.","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.","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.","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.","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."},"title":"Boosting variational inference: An optimization perspective","date_updated":"2024-10-14T12:29:27Z","department":[{"_id":"FrLo"}],"month":"04"},{"oa_version":"Preprint","volume":31,"day":"06","external_id":{"arxiv":["1806.02185"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"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."}],"conference":{"end_date":"2018-12-08","name":"NeurIPS: Neural Information Processing Systems","location":"Montreal, Canada","start_date":"2018-12-03"},"date_published":"2018-06-06T00:00:00Z","year":"2018","citation":{"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.","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.","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.","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."},"publication_status":"published","publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"article_processing_charge":"No","publisher":"Neural Information Processing Systems Foundation","date_updated":"2023-09-13T07:38:24Z","department":[{"_id":"FrLo"}],"month":"06","title":"Boosting black box variational inference","status":"public","scopus_import":"1","date_created":"2023-08-22T14:15:40Z","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"intvolume":"        31","oa":1,"_id":"14202","arxiv":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Gideon","last_name":"Dresdner","full_name":"Dresdner, Gideon"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"first_name":"Isabel","last_name":"Valera","full_name":"Valera, Isabel"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"}],"type":"conference"},{"day":"15","oa_version":"Preprint","volume":80,"quality_controlled":"1","external_id":{"arxiv":["1804.08544"]},"alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"abstract":[{"lang":"eng","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."}],"conference":{"start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"date_published":"2018-07-15T00:00:00Z","year":"2018","citation":{"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.","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.","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.","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.","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","article_processing_charge":"No","publisher":"ML Research Press","date_updated":"2023-09-13T08:13:39Z","department":[{"_id":"FrLo"}],"month":"07","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","status":"public","date_created":"2023-08-22T14:16:01Z","publication":"Proceedings of the 35th International Conference on Machine Learning","language":[{"iso":"eng"}],"intvolume":"        80","page":"5727-5736","oa":1,"_id":"14203","arxiv":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"first_name":"Olivier","full_name":"Fercoq, Olivier","last_name":"Fercoq"},{"last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Cevher","full_name":"Cevher, Volkan","first_name":"Volkan"}],"type":"conference"},{"oa_version":"Preprint","volume":80,"day":"01","quality_controlled":"1","external_id":{"arxiv":["1803.09539"]},"alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"abstract":[{"lang":"eng","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."}],"citation":{"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.","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.","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.","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.","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.","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.","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."},"date_published":"2018-07-01T00:00:00Z","year":"2018","publication_status":"published","publisher":"ML Research Press","article_processing_charge":"No","department":[{"_id":"FrLo"}],"month":"07","date_updated":"2024-10-14T12:29:40Z","title":"On matching pursuit and coordinate descent","date_created":"2023-08-22T14:16:25Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Proceedings of the 35th International Conference on Machine Learning","page":"3198-3207","intvolume":"        80","oa":1,"_id":"14204","arxiv":1,"extern":"1","type":"conference","author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"first_name":"Anant","last_name":"Raj","full_name":"Raj, Anant"},{"first_name":"Sai Praneeth","last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Sebastian U.","full_name":"Stich, Sebastian U.","last_name":"Stich"},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Clustering meets implicit generative models","extern":"1","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Damien","last_name":"Vincent","full_name":"Vincent, Damien"},{"first_name":"Ilya","last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya"},{"first_name":"Gunnar","full_name":"Ratsch, Gunnar","last_name":"Ratsch"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Scholkopf","full_name":"Scholkopf, Bernhard","first_name":"Bernhard"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","date_updated":"2024-10-14T12:30:32Z","month":"05","department":[{"_id":"FrLo"}],"_id":"14224","publication_status":"published","article_processing_charge":"No","arxiv":1,"oa":1,"year":"2018","date_published":"2018-05-01T00:00:00Z","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.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 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.","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.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” <i>6th International Conference on Learning Representations</i>, 2018.","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."},"conference":{"name":"International Conference on Machine Learning","end_date":"2018-05-03","location":"Vancouver, Canada","start_date":"2018-04-30"},"main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"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"}],"external_id":{"arxiv":["1804.11130"]},"quality_controlled":"1","publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","oa_version":"Preprint","scopus_import":"1","status":"public","date_created":"2023-08-22T14:25:34Z"},{"conference":{"start_date":"2018-07-09","location":"Oxford, United Kingdom","end_date":"2018-07-12","name":"LICS: Logic in Computer Science"},"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"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"quality_controlled":"1","external_id":{"isi":["000545262800020"],"arxiv":["1804.10985"]},"alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"day":"09","volume":"F138033","oa_version":"Preprint","ec_funded":1,"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","isi":1,"month":"07","department":[{"_id":"KrCh"}],"date_updated":"2025-06-04T08:04:55Z","publication_status":"published","doi":"10.1145/3209108.3209191","article_processing_charge":"No","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"publisher":"IEEE","citation":{"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>","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, 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>.","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>","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.","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>.","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."},"year":"2018","date_published":"2018-07-09T00:00:00Z","page":"185 - 194","publist_id":"7780","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:51Z","scopus_import":"1","status":"public","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"first_name":"Petr","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny"},{"first_name":"Dominik","last_name":"Velan","full_name":"Velan, Dominik"},{"first_name":"Florian","last_name":"Zuleger","full_name":"Zuleger, Florian"}],"_id":"143","arxiv":1,"oa":1},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1804.11130"}],"abstract":[{"lang":"eng","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."}],"external_id":{"arxiv":["1804.11130"]},"publication":"arXiv","language":[{"iso":"eng"}],"day":"30","oa_version":"Preprint","date_created":"2023-09-13T12:20:49Z","status":"public","title":"Competitive training of mixtures of independent deep generative models","extern":"1","author":[{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello"},{"full_name":"Vincent, Damien","last_name":"Vincent","first_name":"Damien"},{"first_name":"Ilya","last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Sylvain","full_name":"Gelly, Sylvain","last_name":"Gelly"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"}],"article_number":"1804.11130","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","date_updated":"2024-10-14T12:31:09Z","month":"04","department":[{"_id":"FrLo"}],"_id":"14327","publication_status":"submitted","article_processing_charge":"No","doi":"10.48550/arXiv.1804.11130","arxiv":1,"year":"2018","oa":1,"date_published":"2018-04-30T00:00:00Z","citation":{"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.","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>.","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>","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","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>"}},{"alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"language":[{"iso":"eng"}],"external_id":{"isi":["000545262800041"]},"quality_controlled":"1","date_created":"2018-12-11T11:44:52Z","scopus_import":"1","status":"public","volume":"Part F138033","oa_version":"None","day":"09","publist_id":"7779","page":"394 - 403","conference":{"start_date":"2018-07-09","location":"Oxford, UK","end_date":"2018-07-12","name":"LICS: Logic in Computer Science"},"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."}],"doi":"10.1145/3209108.3209194","article_processing_charge":"No","publisher":"IEEE","publication_status":"published","_id":"144","citation":{"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>.","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","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>","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.","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>.","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."},"date_published":"2018-07-09T00:00:00Z","year":"2018","type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-5199-3143","first_name":"Thomas","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"last_name":"Saraç","full_name":"Saraç, Ege","first_name":"Ege"}],"isi":1,"title":"A theory of register monitors","department":[{"_id":"ToHe"}],"month":"07","date_updated":"2023-09-08T11:49:13Z"},{"article_processing_charge":"No","publication_identifier":{"issn":["0261-4189"]},"publisher":"Wiley","doi":"10.15252/embj.201798044","publication_status":"published","year":"2018","date_published":"2018-08-01T00:00:00Z","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>.","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>","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>","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>.","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.","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."},"isi":1,"article_number":"e98044","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","date_updated":"2024-10-09T20:58:32Z","month":"08","department":[{"_id":"JoDa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"volume":37,"oa_version":"Published Version","day":"01","article_type":"original","abstract":[{"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.","lang":"eng"}],"_id":"145","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M"},{"first_name":"Abhiyan","full_name":"Viplav, Abhiyan","last_name":"Viplav"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"first_name":"Angela","full_name":"Vogts, Angela","last_name":"Vogts"},{"first_name":"Annette","full_name":"Denker, Annette","last_name":"Denker"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"full_name":"Fornasiero, Eugenio","last_name":"Fornasiero","first_name":"Eugenio"},{"first_name":"Silvio","full_name":"Rizzoli, Silvio","last_name":"Rizzoli"}],"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).","type":"journal_article","corr_author":"1","issue":"15","file_date_updated":"2020-07-14T12:44:56Z","publication":"The EMBO Journal","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","date_created":"2018-12-11T11:44:52Z","scopus_import":"1","publist_id":"7778","intvolume":"        37","pmid":1,"ddc":["570"],"file":[{"creator":"dernst","file_id":"5710","file_name":"2018_EMBO_Truckenbrodt.pdf","date_updated":"2020-07-14T12:44:56Z","content_type":"application/pdf","access_level":"open_access","file_size":2846470,"relation":"main_file","date_created":"2018-12-17T14:17:29Z","checksum":"a540feb6c9af6aefc78de531461a8835"}]},{"status":"public","date_created":"2018-12-11T11:44:52Z","scopus_import":"1","publication":"Nature Plants","language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["580"],"file":[{"access_level":"open_access","file_size":226829,"relation":"main_file","date_created":"2019-11-18T16:24:07Z","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","creator":"dernst","file_id":"7043","date_updated":"2020-07-14T12:44:56Z","file_name":"2018_NaturePlants_Shi.pdf","content_type":"application/pdf"}],"publist_id":"7777","intvolume":"         4","pmid":1,"page":"596 - 604","oa":1,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"_id":"146","issue":"8","file_date_updated":"2020-07-14T12:44:56Z","author":[{"first_name":"Chun Lin","full_name":"Shi, Chun Lin","last_name":"Shi"},{"orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ullrich","full_name":"Herrmann, Ullrich","last_name":"Herrmann"},{"last_name":"Wildhagen","full_name":"Wildhagen, Mari","first_name":"Mari"},{"id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan","last_name":"Kulik","first_name":"Ivan"},{"last_name":"Kopf","full_name":"Kopf, Andreas","first_name":"Andreas"},{"full_name":"Ishida, Takashi","last_name":"Ishida","first_name":"Takashi"},{"last_name":"Olsson","full_name":"Olsson, Vilde","first_name":"Vilde"},{"last_name":"Anker","full_name":"Anker, Mari Kristine","first_name":"Mari Kristine"},{"last_name":"Albert","full_name":"Albert, Markus","first_name":"Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"first_name":"Georg","full_name":"Felix, Georg","last_name":"Felix"},{"first_name":"Shinichiro","last_name":"Sawa","full_name":"Sawa, Shinichiro"},{"last_name":"Claassen","full_name":"Claassen, Manfred","first_name":"Manfred"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Reidunn B","full_name":"Aalen, Reidunn B","last_name":"Aalen"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","volume":4,"day":"30","oa_version":"Submitted Version","external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"date_published":"2018-07-30T00:00:00Z","year":"2018","citation":{"mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604."},"publisher":"Nature Publishing Group","article_processing_charge":"No","doi":"10.1038/s41477-018-0212-z","publication_status":"published","date_updated":"2023-09-19T10:08:45Z","month":"07","department":[{"_id":"JiFr"}],"isi":1,"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling"},{"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"quality_controlled":"1","ec_funded":1,"oa_version":"Published Version","volume":30,"day":"12","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"doi":"10.1105/tpc.18.00127","publication_identifier":{"issn":["1040-4651"]},"publisher":"Oxford University Press","article_processing_charge":"No","publication_status":"published","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572."},"date_published":"2018-11-12T00:00:00Z","year":"2018","isi":1,"title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","department":[{"_id":"JiFr"}],"month":"11","date_updated":"2025-04-14T07:45:02Z","language":[{"iso":"eng"}],"publication":"The Plant Cell","scopus_import":"1","date_created":"2018-12-11T11:44:52Z","status":"public","publist_id":"7776","page":"2553 - 2572","pmid":1,"intvolume":"        30","_id":"147","oa":1,"type":"journal_article","author":[{"first_name":"Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"first_name":"Glenn R","full_name":"Hicks, Glenn R","last_name":"Hicks"},{"first_name":"Wim","full_name":"Nerinckx, Wim","last_name":"Nerinckx"},{"last_name":"Mishev","full_name":"Mishev, Kiril","first_name":"Kiril"},{"first_name":"Francois","last_name":"Peurois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"last_name":"De","full_name":"De, Rycke Riet Maria","first_name":"Rycke Riet Maria"},{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","issue":"10","corr_author":"1"},{"oa":1,"arxiv":1,"_id":"18","issue":"10","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"status":"public","scopus_import":"1","date_created":"2018-12-11T11:44:11Z","language":[{"iso":"eng"}],"publication":"Ars Combinatoria","publist_id":"8037","page":"269 - 304","intvolume":"       141","citation":{"short":"V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.","apa":"Kolmogorov, V., &#38; Rolinek, M. (2018). Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. Charles Babbage Research Centre.","ama":"Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. 2018;141(10):269-304.","chicago":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>. Charles Babbage Research Centre, 2018.","ista":"Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304.","ieee":"V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” <i>Ars Combinatoria</i>, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018.","mla":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304."},"year":"2018","date_published":"2018-10-01T00:00:00Z","publisher":"Charles Babbage Research Centre","publication_identifier":{"issn":["0381-7032"]},"article_processing_charge":"No","publication_status":"published","department":[{"_id":"VlKo"}],"month":"10","date_updated":"2023-09-19T14:46:18Z","isi":1,"title":"Superconcentrators of density 25.3","volume":141,"oa_version":"Preprint","day":"01","quality_controlled":"1","external_id":{"isi":["000446809500022"],"arxiv":["1405.7828"]},"abstract":[{"lang":"eng","text":"An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17]."}],"main_file_link":[{"url":"https://arxiv.org/abs/1405.7828","open_access":"1"}]},{"abstract":[{"lang":"eng","text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density."}],"article_type":"original","oa_version":"Published Version","day":"01","volume":5,"ec_funded":1,"quality_controlled":"1","external_id":{"arxiv":["1705.10676"]},"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"date_updated":"2025-04-14T07:26:59Z","department":[{"_id":"RoSe"}],"month":"07","title":"Statistical mechanics of the uniform electron gas","date_published":"2018-07-01T00:00:00Z","year":"2018","citation":{"chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2018. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>.","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2018;5:79-116. doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>","apa":"Lewi, M., Lieb, É., &#38; Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>.","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116."},"publication_status":"published","publisher":"Ecole Polytechnique","publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"article_processing_charge":"No","doi":"10.5802/jep.64","file":[{"file_id":"5726","creator":"dernst","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","date_updated":"2020-07-14T12:45:16Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":843938,"date_created":"2018-12-17T16:38:18Z","checksum":"1ba7cccdf3900f42c4f715ae75d6813c"}],"ddc":["510"],"intvolume":"         5","page":"79 - 116","publist_id":"7741","status":"public","date_created":"2018-12-11T11:45:03Z","scopus_import":"1","has_accepted_license":"1","publication":"Journal de l'Ecole Polytechnique - Mathematiques","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Lewi","full_name":"Lewi, Mathieu","first_name":"Mathieu"},{"full_name":"Lieb, Élliott","last_name":"Lieb","first_name":"Élliott"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","type":"journal_article","oa":1,"_id":"180","arxiv":1},{"scopus_import":"1","date_created":"2018-12-11T11:45:03Z","status":"public","publication":"SIAM Journal on Mathematical Analysis","language":[{"iso":"eng"}],"page":"3271 - 3290","intvolume":"        50","publist_id":"7740","oa":1,"_id":"181","arxiv":1,"issue":"3","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","author":[{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","first_name":"Torben H"},{"id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","full_name":"Renfrew, David T","last_name":"Renfrew","orcid":"0000-0003-3493-121X","first_name":"David T"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","oa_version":"Published Version","day":"01","volume":50,"ec_funded":1,"external_id":{"arxiv":["1708.01546"],"isi":["000437018500032"]},"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"Structured Non-Hermitian Random Matrices","call_identifier":"FWF","_id":"258F40A4-B435-11E9-9278-68D0E5697425","grant_number":"M02080"}],"abstract":[{"text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.01546","open_access":"1"}],"year":"2018","date_published":"2018-01-01T00:00:00Z","citation":{"short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","apa":"Erdös, L., Krüger, T. H., &#38; Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/17M1143125\">https://doi.org/10.1137/17M1143125</a>","ama":"Erdös L, Krüger TH, Renfrew DT. 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Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:<a href=\"https://doi.org/10.1137/17M1143125\">10.1137/17M1143125</a>."},"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics ","article_processing_charge":"No","doi":"10.1137/17M1143125","date_updated":"2025-04-15T08:05:02Z","month":"01","department":[{"_id":"LaEr"}],"title":"Power law decay for systems of randomly coupled differential equations","isi":1},{"page":"177 - 186","publist_id":"7739","file":[{"file_id":"7833","creator":"dernst","file_name":"2018_HSCC_Bakhirkin.pdf","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":5900421,"date_created":"2020-05-14T12:18:29Z","checksum":"81eabc96430e84336ea88310ac0a1ad0"}],"ddc":["000"],"has_accepted_license":"1","publication":"Proceedings of the 21st International Conference on Hybrid Systems","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:45:04Z","status":"public","scopus_import":"1","author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","file_date_updated":"2020-07-14T12:45:17Z","_id":"182","oa":1,"conference":{"start_date":"2018-04-11","location":"Porto, Portugal","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2018-04-13"},"abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"quality_controlled":"1","external_id":{"isi":["000474781600020"]},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"alternative_title":["HSCC Proceedings"],"day":"11","oa_version":"Submitted Version","title":"Efficient parametric identification for STL","isi":1,"date_updated":"2025-07-10T11:51:21Z","department":[{"_id":"ToHe"}],"month":"04","publication_status":"published","publisher":"ACM","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"article_processing_charge":"No","doi":"10.1145/3178126.3178132","year":"2018","date_published":"2018-04-11T00:00:00Z","citation":{"ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems - Computation and Control, HSCC Proceedings, , 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, ACM, 2018, pp. 177–86, doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, Porto, Portugal, 2018, pp. 177–186.","apa":"Bakhirkin, A., Ferrere, T., &#38; Maler, O. (2018). Efficient parametric identification for STL. In <i>Proceedings of the 21st International Conference on Hybrid Systems</i> (pp. 177–186). Porto, Portugal: ACM. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, 177–86. ACM, 2018. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: <i>Proceedings of the 21st International Conference on Hybrid Systems</i>. ACM; 2018:177-186. doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>"}},{"_id":"183","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Manjunath, Niveditha","last_name":"Manjunath","first_name":"Niveditha"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","date_created":"2018-12-11T11:45:04Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"publist_id":"7738","page":"197 - 206","citation":{"ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems - Computation and Control, HSCC Proceedings, , 197–206.","mla":"Bartocci, Ezio, et al. <i>Localizing Faults in Simulink/Stateflow Models with STL</i>. Association for Computing Machinery, 2018, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>.","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems - Computation and Control, Porto, Portugal, 2018, pp. 197–206.","apa":"Bartocci, E., Ferrere, T., Manjunath, N., &#38; Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems - Computation and Control, Porto, Portugal: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, 2018, pp. 197–206.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, 2018. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>.","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery; 2018:197-206. doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>"},"date_published":"2018-04-11T00:00:00Z","year":"2018","doi":"10.1145/3178126.3178131","article_processing_charge":"No","publisher":"Association for Computing Machinery","publication_status":"published","month":"04","department":[{"_id":"ToHe"}],"date_updated":"2025-07-10T11:51:22Z","isi":1,"title":"Localizing faults in simulink/stateflow models with STL","day":"11","oa_version":"None","alternative_title":["HSCC Proceedings"],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","external_id":{"isi":["000474781600022"]},"abstract":[{"lang":"eng","text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain."}],"conference":{"end_date":"2018-04-13","name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2018-04-11","location":"Porto, Portugal"}}]