[{"abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"publist_id":"5082","issue":"May-June","type":"journal_article","author":[{"full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren","first_name":"Patrik"}],"date_created":"2018-12-11T11:55:07Z","date_updated":"2021-01-12T06:54:35Z","volume":"68/Part 2","oa_version":"Preprint","_id":"1997","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","status":"public","publication_status":"published","title":"The three-state toric homogeneous Markov chain model has Markov degree two","publisher":"Elsevier","department":[{"_id":"CaUh"}],"day":"01","month":"05","scopus_import":1,"date_published":"2015-05-01T00:00:00Z","doi":"10.1016/j.jsc.2014.09.014","language":[{"iso":"eng"}],"publication":"Journal of Symbolic Computation","citation":{"ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296. doi:10.1016/j.jsc.2014.09.014","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014."},"main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"oa":1,"quality_controlled":"1","page":"285 - 296"},{"page":"832 - 847","citation":{"mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:10.1111/sjos.12139.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","apa":"Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139"},"publication":"Scandinavian Journal of Statistics","date_published":"2015-09-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 42","title":"Iterative scaling in curved exponential families","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2008","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/sjos.12139","month":"09","department":[{"_id":"CaUh"}],"publisher":"Wiley","publication_status":"published","year":"2015","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","volume":42,"date_updated":"2021-01-12T06:54:41Z","date_created":"2018-12-11T11:55:11Z","author":[{"full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"publist_id":"5068"},{"oa_version":"Preprint","intvolume":" 24","title":"The monotone secant conjecture in the real Schubert calculus","status":"public","_id":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. "}],"type":"journal_article","date_published":"2015-06-23T00:00:00Z","page":"261 - 269","citation":{"ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” Experimental Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 2015;24(3):261-269. doi:10.1080/10586458.2014.980044","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis, 2015, pp. 261–69, doi:10.1080/10586458.2014.980044."},"publication":"Experimental Mathematics","article_processing_charge":"No","day":"23","scopus_import":1,"volume":24,"date_updated":"2021-01-12T06:54:40Z","date_created":"2018-12-11T11:55:10Z","author":[{"full_name":"Hein, Nicolas","last_name":"Hein","first_name":"Nicolas"},{"full_name":"Hillar, Christopher","first_name":"Christopher","last_name":"Hillar"},{"full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sottile","first_name":"Frank","full_name":"Sottile, Frank"},{"first_name":"Zach","last_name":"Teitler","full_name":"Teitler, Zach"}],"department":[{"_id":"CaUh"}],"publisher":"Taylor & Francis","publication_status":"published","year":"2015","publist_id":"5070","language":[{"iso":"eng"}],"doi":"10.1080/10586458.2014.980044","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"month":"06"},{"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"citation":{"chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.","apa":"Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. Elsevier. https://doi.org/10.1016/j.csda.2015.01.017","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” Computational Statistics & Data Analysis, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72. doi:10.1016/j.csda.2015.01.017"},"publication":"Computational Statistics & Data Analysis","page":"57 - 72","quality_controlled":"1","date_published":"2015-07-01T00:00:00Z","doi":"10.1016/j.csda.2015.01.017","language":[{"iso":"eng"}],"scopus_import":1,"month":"07","day":"01","_id":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","intvolume":" 87","department":[{"_id":"CaUh"}],"publisher":"Elsevier","publication_status":"published","title":"Faithfulness and learning hypergraphs from discrete distributions","status":"public","author":[{"full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"volume":87,"oa_version":"Preprint","date_created":"2018-12-11T11:55:13Z","date_updated":"2021-01-12T06:54:43Z","type":"journal_article","issue":"7","publist_id":"5062","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}]},{"type":"journal_article","issue":"1","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}],"intvolume":" 1853","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2025","file":[{"access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","creator":"system","content_type":"application/pdf","file_size":926685,"file_id":"4936","relation":"main_file","checksum":"5bb328edebb6a91337cadd7d63f961b7","date_created":"2018-12-12T10:12:18Z","date_updated":"2020-07-14T12:45:25Z"}],"oa_version":"Submitted Version","pubrep_id":"615","scopus_import":1,"has_accepted_license":"1","day":"01","page":"144 - 156","citation":{"chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.","ieee":"D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009"},"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","date_published":"2015-01-01T00:00:00Z","publist_id":"5047","file_date_updated":"2020-07-14T12:45:25Z","publisher":"Elsevier","department":[{"_id":"DaSi"}],"publication_status":"published","year":"2015","volume":1853,"date_created":"2018-12-11T11:55:17Z","date_updated":"2021-01-12T06:54:48Z","author":[{"full_name":"Kawada, Daiki","first_name":"Daiki","last_name":"Kawada"},{"first_name":"Hiromu","last_name":"Kobayashi","full_name":"Kobayashi, Hiromu"},{"first_name":"Tsuyoshi","last_name":"Tomita","full_name":"Tomita, Tsuyoshi"},{"full_name":"Nakata, Eisuke","first_name":"Eisuke","last_name":"Nakata"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"full_name":"Toshimaa, Jiro","first_name":"Jiro","last_name":"Toshimaa"}],"month":"01","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.bbamcr.2014.10.009"},{"scopus_import":1,"day":"01","month":"01","page":"1 - 11","quality_controlled":"1","citation":{"ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” Computers and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"publication":"Computers and Fluids","language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","doi":"10.1016/j.compfluid.2014.09.021","type":"journal_article","publist_id":"5042","issue":"1","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"department":[{"_id":"BjHo"}],"intvolume":" 106","publisher":"Elsevier","status":"public","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","publication_status":"published","year":"2015","_id":"2030","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","volume":106,"date_updated":"2021-01-12T06:54:51Z","date_created":"2018-12-11T11:55:18Z","author":[{"full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rampp, Markus","first_name":"Markus","last_name":"Rampp"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}]},{"issue":"5","abstract":[{"text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1317546,"file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:10Z","date_updated":"2020-07-14T12:45:26Z","checksum":"3566f3a8b0c1bc550e62914a88c584ff","file_id":"4670","relation":"main_file"}],"pubrep_id":"486","intvolume":" 15","ddc":["000"],"title":"The persistent homology of a self-map","status":"public","_id":"2035","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2015-10-01T00:00:00Z","page":"1213 - 1244","citation":{"ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","apa":"Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:10.1007/s10208-014-9223-y.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics. Springer, 2015. https://doi.org/10.1007/s10208-014-9223-y."},"publication":"Foundations of Computational Mathematics","publist_id":"5022","ec_funded":1,"file_date_updated":"2020-07-14T12:45:26Z","volume":15,"date_created":"2018-12-11T11:55:20Z","date_updated":"2021-01-12T06:54:53Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866"},{"last_name":"Mrozek","first_name":"Marian","full_name":"Mrozek, Marian"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","year":"2015","month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s10208-014-9223-y","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2034","title":"Probabilistic opacity for Markov decision processes","status":"public","intvolume":" 115","abstract":[{"text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2015-01-01T00:00:00Z","publication":" Information Processing Letters","citation":{"ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59.","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” Information Processing Letters, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","apa":"Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.001","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:10.1016/j.ipl.2014.09.001.","short":"B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115 (2015) 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001."},"page":"52 - 59","day":"01","scopus_import":1,"author":[{"full_name":"Bérard, Béatrice","first_name":"Béatrice","last_name":"Bérard"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Sznajder, Nathalie","first_name":"Nathalie","last_name":"Sznajder"}],"date_created":"2018-12-11T11:55:20Z","date_updated":"2021-01-12T06:54:52Z","volume":115,"year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"ec_funded":1,"publist_id":"5025","doi":"10.1016/j.ipl.2014.09.001","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.4225"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"month":"01"},{"publication":"Archive for Rational Mechanics and Analysis","citation":{"ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.","apa":"Nam, P., & Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-014-0781-6","ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” Archive for Rational Mechanics and Analysis, vol. 215, no. 2. Springer, pp. 381–417, 2015.","ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 2015;215(2):381-417. doi:10.1007/s00205-014-0781-6","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis. Springer, 2015. https://doi.org/10.1007/s00205-014-0781-6.","mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:10.1007/s00205-014-0781-6.","short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1402.1153","open_access":"1"}],"quality_controlled":"1","page":"381 - 417","date_published":"2015-02-01T00:00:00Z","doi":"10.1007/s00205-014-0781-6","language":[{"iso":"eng"}],"scopus_import":1,"month":"02","day":"01","_id":"2085","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Collective excitations of Bose gases in the mean-field regime","publisher":"Springer","department":[{"_id":"RoSe"}],"intvolume":" 215","author":[{"last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"date_updated":"2021-01-12T06:55:13Z","date_created":"2018-12-11T11:55:37Z","volume":215,"oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. "}],"publist_id":"4951","issue":"2"},{"scopus_import":1,"month":"02","day":"01","quality_controlled":"1","page":"1365 - 1416","publication":"Communications in Mathematical Physics","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5106"}],"citation":{"ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 2015;333(3):1365-1416. doi:10.1007/s00220-014-2119-5","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2119-5","ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” Communications in Mathematical Physics, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416.","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:10.1007/s00220-014-2119-5.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-014-2119-5."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00220-014-2119-5","date_published":"2015-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). "}],"issue":"3","publist_id":"4818","title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","publication_status":"published","status":"public","department":[{"_id":"LaEr"}],"publisher":"Springer","intvolume":" 333","_id":"2166","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_created":"2018-12-11T11:56:05Z","date_updated":"2021-01-12T06:55:43Z","volume":333,"oa_version":"Preprint","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"}]}]