一个高通量和用户友好的计算工具,用于量化和可视化图像数据集中的对称变化。

IF 2.3 4区 数学 Q2 BIOLOGY
Liam D O'Brien, Punit Gandhi, Maria-Veronica Ciocanel, Adriana T Dawes
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引用次数: 0

摘要

对称是生物系统的基本属性,但它通常被简化为离散的、主观的分类,无法捕捉到真实生物体中对称的连续和渐变性质。我们提出了一个高通量,用户友好的计算框架,用于量化和可视化生物对称性作为使用转换信息(t1)的连续变量,这是一种量化对象与其转换自我之间分歧的信息理论度量。我们建立了t1的关键数学属性,包括不变性、等变性和Lipschitz连续性,保证了平移、旋转、反射和重新缩放等变换的鲁棒性,从而实现了跨异构图像数据集的可靠对称量化,而无需手动标记或图像对齐。在此理论基础上,我们介绍了一个计算管道,它可以自动检测对称中心,计算t1曲线,并使用功能主成分分析(fPCA)实现对称数据的可视化。我们在两个生物数据集上展示了该框架的实用性:一个是被子植物花图像的大集合,在那里我们研究旋转和反射对称性;另一个是模拟蕨类图像的数据集,在那里我们研究缩放和平移下的分形自相似性。我们对花卉数据集的分析提供了趋同进化的新证据。在这两个数据集中,对所得到的t1剖面的fPCA显示,对称性最好被描述为连续体,而不是一组离散类,并且存在传统分类方法无法捕获的微妙形态变化。总之,这些结果表明,T - I为将对称性整合到定量进化、生态和发展模型中提供了数学原则和生物学信息基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A High Throughput and User-Friendly Computational Tool for Quantifying and Visualizing Symmetry Variation in Image Datasets.

Symmetry is a fundamental property of biological systems, yet it is commonly reduced to discrete, subjective classifications that fail to capture the continuous and graded nature of symmetry in real organisms. We present a high-throughput, user-friendly computational framework for quantifying and visualizing biological symmetry as a continuous variable using transformation information ( T I ), an information theoretic measure that quantifies the divergence between an object and its transformed self. We establish key mathematical properties of T I , including invariance, equivariance, and Lipschitz continuity, that guarantee robustness to transformations such as translation, rotation, reflection, and rescaling, enabling reliable symmetry quantification across heterogeneous image datasets without manual landmarking or image alignment. Building on this theoretical foundation, we introduce a computational pipeline that automates symmetry center detection, T I curve computation, and visualization of the symmetry data using functional principal component analysis (fPCA). We demonstrate the utility of this framework on two biological datasets: a large collection of angiosperm flower images, where we investigate rotational and reflectional symmetries, and a dataset of simulated fern images, where we investigate fractal self-similarity under scaling and translation. Our analysis of the floral dataset provides novel evidence of convergent evolution. In both datasets, fPCA of the resulting T I profiles reveals that symmetry is best characterized as a continuum rather than a set of discrete classes, and there is subtle morphological variation that is not captured by traditional categorical approaches. Together, these results suggest that T I provides a mathematically principled and biologically informative foundation for integrating symmetry into quantitative evolutionary, ecological, and developmental models.

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来源期刊
CiteScore
3.90
自引率
8.60%
发文量
123
审稿时长
7.5 months
期刊介绍: The Bulletin of Mathematical Biology, the official journal of the Society for Mathematical Biology, disseminates original research findings and other information relevant to the interface of biology and the mathematical sciences. Contributions should have relevance to both fields. In order to accommodate the broad scope of new developments, the journal accepts a variety of contributions, including: Original research articles focused on new biological insights gained with the help of tools from the mathematical sciences or new mathematical tools and methods with demonstrated applicability to biological investigations Research in mathematical biology education Reviews Commentaries Perspectives, and contributions that discuss issues important to the profession All contributions are peer-reviewed.
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