Lloyd A. Courtenay, Julia Aramendi, Diego González-Aguilera
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引用次数: 0
Abstract
Geometric Morphometrics can be used to describe morphology as a series of coordinates after the effects of variation in translation, rotation, and scale have been removed. This can be further divided into the notion of shape and form, where the latter excludes the scaling procedure from analyses. Dimensionality reduction in Geometric Morphometrics is necessary for the representation of this data into a reduced, more manageable set of dimensions, while preserving as much of the original variation as possible. The purpose of this study is to explore a new means of performing dimensionality reduction on Procrustes landmark data. Here we present a new mathematical model that can be used to enhance dimensionality reduction techniques such as Principal Component Analyses. Integrated into a new R library, the GraphGMM framework uses elements of geometric learning and graph theory to aggregate and embed (project) morphological information from Procrustes coordinates into a new set of transformed coordinates. We validate this model through the use of theoretically constructed, as well as open source, datasets. We finally present a pilot case study using great ape radii to show how these transformed landmarks efficiently capture morphological information, prior to dimensionality reduction, leading to a more efficient construction of a final representation of a morphological coordinate space. Graph-based Geometric Morphometrics thus provides a new insight into the study of morphological patterns, that can be used as an additional source of information in bioanthropological studies.
几何形态计量学可用于将形态描述为去除平移、旋转和比例变化影响后的一系列坐标。这又可进一步分为形状和形态的概念,后者在分析中排除了缩放程序。几何形态计量学中的降维是将这些数据表示为一个缩小的、更易于管理的维数集的必要手段,同时尽可能多地保留原始变化。本研究的目的是探索一种对普罗克斯特地标数据进行降维处理的新方法。在此,我们提出了一种新的数学模型,可用于增强主成分分析等降维技术。GraphGMM 框架集成到一个新的 R 库中,利用几何学习和图论元素将普罗克鲁斯坐标中的形态信息汇总并嵌入到一组新的转换坐标中。我们通过使用理论构建的数据集和开源数据集验证了这一模型。最后,我们利用巨猿半径进行了试点案例研究,展示了这些转换后的地标如何在降维之前有效捕捉形态信息,从而更高效地构建形态坐标空间的最终表示。因此,基于图形的几何形态计量学为形态模式研究提供了新的视角,可作为生物人类学研究的额外信息来源。
期刊介绍:
Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance.
Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.