[{"date_published":"2014-03-20T00:00:00Z","citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.","mla":"Klimova, Anna, and Tamás Rudas. GIPFrm: Generalized Iterative Proportional Fitting for Relational Models. The Comprehensive R Archive Network, 2014.","short":"A. Klimova, T. Rudas, (2014).","ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network.","ieee":"A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.","apa":"Klimova, A., & Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014."},"oa":1,"main_file_link":[{"url":"https://CRAN.R-project.org/package=gIPFrm ","open_access":"1"}],"month":"03","day":"20","article_processing_charge":"No","author":[{"full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"date_created":"2018-12-11T11:55:10Z","date_updated":"2022-08-26T08:12:12Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2007","year":"2014","status":"public","title":"gIPFrm: Generalized iterative proportional fitting for relational models","publisher":"The Comprehensive R Archive Network","department":[{"_id":"CaUh"}],"abstract":[{"text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual","lang":"eng"}],"publist_id":"5069","type":"research_data_reference"},{"scopus_import":1,"day":"10","page":"1079 - 1116","publication":"Foundations of Computational Mathematics","citation":{"ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0","apa":"Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” Foundations of Computational Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.","ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0.","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0."},"date_published":"2014-10-10T00:00:00Z","type":"journal_article","abstract":[{"text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n","lang":"eng"}],"issue":"5","title":"Hypersurfaces and their singularities in partial correlation testing","status":"public","intvolume":" 14","_id":"2013","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"10","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1209.0285","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s10208-014-9205-0","publist_id":"5063","publication_status":"published","department":[{"_id":"CaUh"}],"publisher":"Springer","year":"2014","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020).","date_created":"2018-12-11T11:55:12Z","date_updated":"2021-01-12T06:54:43Z","volume":14,"author":[{"full_name":"Lin, Shaowei","first_name":"Shaowei","last_name":"Lin"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"full_name":"Bühlmann, Peter","first_name":"Peter","last_name":"Bühlmann"}]},{"scopus_import":1,"day":"01","citation":{"mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14.","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","apa":"Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184."},"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"170 - 184","date_published":"2014-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance.","lang":"eng"}],"_id":"2047","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8744","status":"public","title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","oa_version":"Submitted Version","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"external_id":{"arxiv":["1407.8067"]},"project":[{"grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits"}],"quality_controlled":"1","doi":"10.1007/978-3-319-11257-2_14","conference":{"name":"PSD: Privacy in Statistical Databases","end_date":"2014-09-19","location":"Ibiza, Spain","start_date":"2014-09-17"},"language":[{"iso":"eng"}],"publist_id":"5004","year":"2014","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"publisher":"Springer","editor":[{"first_name":"Josep","last_name":"Domingo Ferrer","full_name":"Domingo Ferrer, Josep"}],"publication_status":"published","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"full_name":"Rybar, Michal","first_name":"Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"},{"full_name":"Fienberg, Stephen","last_name":"Fienberg","first_name":"Stephen"}],"volume":8744,"date_created":"2018-12-11T11:55:24Z","date_updated":"2021-01-12T06:54:57Z"},{"day":"01","scopus_import":1,"date_published":"2014-03-01T00:00:00Z","page":"161 - 188","citation":{"chicago":"Haws, David, Abraham Martin del Campo Sanchez, Akimichi Takemura, and Ruriko Yoshida. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie. Springer, 2014. https://doi.org/10.1007/s13366-013-0178-y.","mla":"Haws, David, et al. “Markov Degree of the Three-State Toric Homogeneous Markov Chain Model.” Beitrage Zur Algebra Und Geometrie, vol. 55, no. 1, Springer, 2014, pp. 161–88, doi:10.1007/s13366-013-0178-y.","short":"D. Haws, A. Martin del Campo Sanchez, A. Takemura, R. Yoshida, Beitrage Zur Algebra Und Geometrie 55 (2014) 161–188.","ista":"Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. 2014. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 55(1), 161–188.","apa":"Haws, D., Martin del Campo Sanchez, A., Takemura, A., & Yoshida, R. (2014). Markov degree of the three-state toric homogeneous Markov chain model. Beitrage Zur Algebra Und Geometrie. Springer. https://doi.org/10.1007/s13366-013-0178-y","ieee":"D. Haws, A. Martin del Campo Sanchez, A. Takemura, and R. Yoshida, “Markov degree of the three-state toric homogeneous Markov chain model,” Beitrage zur Algebra und Geometrie, vol. 55, no. 1. Springer, pp. 161–188, 2014.","ama":"Haws D, Martin del Campo Sanchez A, Takemura A, Yoshida R. Markov degree of the three-state toric homogeneous Markov chain model. Beitrage zur Algebra und Geometrie. 2014;55(1):161-188. doi:10.1007/s13366-013-0178-y"},"publication":"Beitrage zur Algebra und Geometrie","issue":"1","abstract":[{"lang":"eng","text":"We consider the three-state toric homogeneous Markov chain model (THMC) without loops and initial parameters. At time T, the size of the design matrix is 6 × 3 · 2T-1 and the convex hull of its columns is the model polytope. We study the behavior of this polytope for T ≥ 3 and we show that it is defined by 24 facets for all T ≥ 5. Moreover, we give a complete description of these facets. From this, we deduce that the toric ideal associated with the design matrix is generated by binomials of degree at most 6. Our proof is based on a result due to Sturmfels, who gave a bound on the degree of the generators of a toric ideal, provided the normality of the corresponding toric variety. In our setting, we established the normality of the toric variety associated to the THMC model by studying the geometric properties of the model polytope."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 55","status":"public","title":"Markov degree of the three-state toric homogeneous Markov chain model","_id":"2178","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s13366-013-0178-y","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1204.3070","open_access":"1"}],"oa":1,"publist_id":"4804","volume":55,"date_updated":"2021-01-12T06:55:48Z","date_created":"2018-12-11T11:56:10Z","author":[{"last_name":"Haws","first_name":"David","full_name":"Haws, David"},{"full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Takemura, Akimichi","first_name":"Akimichi","last_name":"Takemura"},{"last_name":"Yoshida","first_name":"Ruriko","full_name":"Yoshida, Ruriko"}],"publisher":"Springer","department":[{"_id":"CaUh"}],"publication_status":"published","acknowledgement":"Research of Martín del Campo supported in part by NSF Grant DMS-915211.","year":"2014"},{"abstract":[{"lang":"eng","text":"The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice."}],"publist_id":"5064","article_number":"1401.0468","type":"preprint","date_created":"2018-12-11T11:55:12Z","date_updated":"2023-10-18T08:06:45Z","oa_version":"Submitted Version","author":[{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"}],"publication_status":"submitted","title":"Sphere packing with limited overlap","status":"public","department":[{"_id":"HeEd"},{"_id":"CaUh"}],"year":"2014","_id":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper. The second author has been supported by the Max Planck Center for Visual Computing and Communication","day":"01","month":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2014-01-01T00:00:00Z","doi":"10.48550/arXiv.1401.0468","publication":"arXiv","citation":{"ista":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468.","ieee":"M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” arXiv. .","apa":"Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468","ama":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv. doi:10.48550/arXiv.1401.0468","chicago":"Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468.","mla":"Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv, 1401.0468, doi:10.48550/arXiv.1401.0468.","short":"M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.)."},"external_id":{"arxiv":["1401.0468"]},"oa":1,"main_file_link":[{"url":"http://cccg.ca/proceedings/2014/papers/paper23.pdf","open_access":"1"}]}]