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Blazquez-Llorca","year":"2010","journal-title":"Front Neuroanat"},{"key":"ref36","article-title":"Brodmann\u2019s Localisation in the Cerebral Cortex","author":"K Brodmann","year":"1994"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1093\/cercor\/7.5.432","article-title":"The occipitoparietal pathway of the macaque monkey: comparison of pyramidal cell morphology in layer III of functionally related cortical visual areas","volume":"7","author":"GN Elston","year":"1997","journal-title":"Cereb Cortex"},{"key":"ref38","doi-asserted-by":"crossref","DOI":"10.1523\/JNEUROSCI.21-17-j0002.2001","article-title":"The pyramidal cell in cognition: A comparative study in human and monkey","volume":"21","author":"GN Elston","year":"2001","journal-title":"J Neurosci"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"11567","DOI":"10.1073\/pnas.1006269107","article-title":"Alterations of cortical pyramidal neurons in mice lacking high-affinity nicotinic 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Voxel-based representation, display and thickness analysis of intricate shapes. Proceedings of the Ninth International Conference on Computer Aided Design and Computer Graphics. 2005.","DOI":"10.1109\/CAD-CG.2005.86"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Lorensen WE, Cline HE. Marching cubes: A high resolution 3D surface construction algorithm. Proceedings of the 14th Annual Conference on Computer Graphics and Interactive Techniques. 1987. pp. 163\u2013169.","DOI":"10.1145\/37401.37422"},{"key":"ref42","doi-asserted-by":"crossref","unstructured":"Desbrun M, Meyer M, Schr\u00f6der P, Barr AH. Implicit fairing of irregular meshes using diffusion and curvature flow. Proceedings of the 26th Annual Conference on Computer Graphics and Interactive Techniques. 1999. pp. 317\u2013324.","DOI":"10.1145\/311535.311576"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1007\/s11042-007-0181-0","article-title":"A survey of content based 3D shape retrieval methods","volume":"39","author":"JW Tangelder","year":"2008","journal-title":"Multimed Tools Appl"},{"key":"ref44","doi-asserted-by":"crossref","unstructured":"Hilaga M, Shinagawa Y, Kohmura T, Kunii TL. Topology matching for fully automatic similarity estimation of 3D shapes. Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques. 2001. pp. 203\u2013212.","DOI":"10.1145\/383259.383282"},{"key":"ref45","article-title":"Mixture Models: Inference and Applications to Clustering","author":"GJ McLachlan","year":"1988"},{"key":"ref46","article-title":"Statistical Analysis of Finite Mixture Distributions","author":"DM Titterington","year":"1985"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum likelihood from incomplete data via the EM algorithm","volume":"39","author":"AP Dempster","year":"1977","journal-title":"J R Stat Soc Ser B"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the dimension of a model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Stat"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1198\/016214502760047131","article-title":"Model-based clustering, discriminant analysis, and density estimation","volume":"97","author":"C Fraley","year":"2002","journal-title":"J Am Stat Assoc"},{"key":"ref50","doi-asserted-by":"crossref","unstructured":"Cohen W. Fast effective rule induction. Proceedings of the Twelfth International Conference on Machine Learning. 1995. pp. 115\u2013123.","DOI":"10.1016\/B978-1-55860-377-6.50023-2"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1613\/jair.953","article-title":"SMOTE: Synthetic minority over-sampling technique","volume":"16","author":"V Chawla N","year":"2002","journal-title":"J Artif Intell Res"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1145\/1656274.1656278","article-title":"The WEKA data mining software: An update","volume":"11","author":"M Hall","year":"2009","journal-title":"SIGKDD Explor"},{"key":"ref53","unstructured":"Abou-Moustafa, Ferrie FP. A note on metric properties of some divergence measures: The Gaussian case. Proceedings of Machine Learning Research. 2012. pp. 1\u201312."},{"key":"ref54","article-title":"Theory and Methods of Scaling","author":"WS Torgerson","year":"1958"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1198\/jcgs.2009.08054","article-title":"Simulating data to study performance of finite mixture modeling and clustering algorithms","volume":"19","author":"R Maitra","year":"2010","journal-title":"J Comput Graph Stat"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v051.i12","article-title":"MixSim: An R package for simulating data to study performance of clustering algorithms","volume":"51","author":"V Melnykov","year":"2012","journal-title":"J Stat Softw"},{"key":"ref57","author":"C Loop","year":"1987"},{"key":"ref58","unstructured":"Kohavi R. A study of cross-validation and bootstrap for accuracy estimation and model selection. Proceedings of the 14th International Joint Conference on Artificial Intelligence. 1995. pp. 1137\u20131143."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006221","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,7,24]],"date-time":"2018-07-24T00:00:00Z","timestamp":1532390400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006221","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,7]],"date-time":"2024-07-07T14:20:17Z","timestamp":1720362017000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006221"}},"subtitle":[],"editor":[{"given":"Hermann","family":"Cuntz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,6,13]]},"references-count":58,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2018,6,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006221","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006221","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,13]]}}}