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Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data

In this study, we tested the hypothesis that machine learning methods can accurately classify extant primates based on triquetrum shape data. We then used this classification tool to observe the affinities between extant primates and fossil hominoids. We assessed the discrimination accuracy for an u...

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Autores principales: Vanhoof, Marie J. M., Croquet, Balder, De Groote, Isabelle, Vereecke, Evie E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509576/
https://www.ncbi.nlm.nih.gov/pubmed/37736524
http://dx.doi.org/10.1098/rsos.230950
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author Vanhoof, Marie J. M.
Croquet, Balder
De Groote, Isabelle
Vereecke, Evie E.
author_facet Vanhoof, Marie J. M.
Croquet, Balder
De Groote, Isabelle
Vereecke, Evie E.
author_sort Vanhoof, Marie J. M.
collection PubMed
description In this study, we tested the hypothesis that machine learning methods can accurately classify extant primates based on triquetrum shape data. We then used this classification tool to observe the affinities between extant primates and fossil hominoids. We assessed the discrimination accuracy for an unsupervised and supervised learning pipeline, i.e. with principal component analysis (PCA) and linear discriminant analysis (LDA) feature extraction, when tasked with the classification of extant primates. The trained algorithm is used to classify a sample of known fossil hominoids. For the visualization, PCA and uniform manifold approximation and projection (UMAP) are used. The results show that the discriminant function correctly classified the extant specimens with an F1-score of 0.90 for both PCA and LDA. In addition, the classification of fossil hominoids reflects taxonomy and locomotor behaviour reported in literature. This classification based on shape data using PCA and LDA is a powerful tool that can discriminate between the triquetrum shape of extant primates with high accuracy and quantitatively compare fossil and extant morphology. It can be used to support taxonomic differentiation and aid the further interpretation of fossil remains. Further testing is necessary by including other bones and more species and specimens per species extinct primates.
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spelling pubmed-105095762023-09-21 Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data Vanhoof, Marie J. M. Croquet, Balder De Groote, Isabelle Vereecke, Evie E. R Soc Open Sci Organismal and Evolutionary Biology In this study, we tested the hypothesis that machine learning methods can accurately classify extant primates based on triquetrum shape data. We then used this classification tool to observe the affinities between extant primates and fossil hominoids. We assessed the discrimination accuracy for an unsupervised and supervised learning pipeline, i.e. with principal component analysis (PCA) and linear discriminant analysis (LDA) feature extraction, when tasked with the classification of extant primates. The trained algorithm is used to classify a sample of known fossil hominoids. For the visualization, PCA and uniform manifold approximation and projection (UMAP) are used. The results show that the discriminant function correctly classified the extant specimens with an F1-score of 0.90 for both PCA and LDA. In addition, the classification of fossil hominoids reflects taxonomy and locomotor behaviour reported in literature. This classification based on shape data using PCA and LDA is a powerful tool that can discriminate between the triquetrum shape of extant primates with high accuracy and quantitatively compare fossil and extant morphology. It can be used to support taxonomic differentiation and aid the further interpretation of fossil remains. Further testing is necessary by including other bones and more species and specimens per species extinct primates. The Royal Society 2023-09-20 /pmc/articles/PMC10509576/ /pubmed/37736524 http://dx.doi.org/10.1098/rsos.230950 Text en © 2023 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Organismal and Evolutionary Biology
Vanhoof, Marie J. M.
Croquet, Balder
De Groote, Isabelle
Vereecke, Evie E.
Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title_full Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title_fullStr Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title_full_unstemmed Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title_short Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
title_sort principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data
topic Organismal and Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509576/
https://www.ncbi.nlm.nih.gov/pubmed/37736524
http://dx.doi.org/10.1098/rsos.230950
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