统一相似性度量标准,让不同研究结果可比。
A Framework for Standardizing Similarity Measures in a Rapidly Evolving Field
- 构建可扩展的Python框架,整合100种相似性度量方法
- 涵盖14个工具包,支持对齐生物与人工系统的评估
- 提供灵活命名机制,适应领域快速演化
相似性度量是量化人工系统与生物系统之间对齐程度的基础工具。然而,度量方法多样、命名和实现方式不统一,导致跨研究比较困难。为此,我们创建并持续维护一个Python代码库,用于基准测试和标准化相似性度量。由于即使常见方法如中心核对齐(CKA)也存在至少12种变体,且该数量随领域发展持续增长,我们不主张固定不变的命名规范。当前仓库包含约100种来自14个软件包的相似性度量,作为当前阶段的实用工具。为应对领域演进,我们提出一套开发、验证和优化命名规范的框架,目标是唯一且高效地指定每种度量,最终促进研究间的可比性。
原文摘要 · Abstract (English)
Similarity measures are fundamental tools for quantifying the alignment between artificial and biological systems. However, the diversity of similarity measures and their varied naming and implementation conventions makes it challenging to compare across studies. To facilitate comparisons and make explicit the implementation choices underlying a given code package, we have created and are continuing to develop a Python repository that benchmarks and standardizes similarity measures. The goal of creating a consistent naming convention that uniquely and efficiently specifies a similarity measure is not trivial as, for example, even commonly used methods like Centered Kernel Alignment (CKA) have at least 12 different variations, and this number will likely continue to grow as the field evolves. For this reason, we do not advocate for a fixed, definitive naming convention. The landscape of similarity measures and best practices will continue to change and so we see our current repository, which incorporates approximately 100 different similarity measures from 14 packages, as providing a useful tool at this snapshot in time. To accommodate the evolution of the field we present a framework for developing, validating, and refining naming conventions with the goal of uniquely and efficiently specifying similarity measures, ultimately making it easier for the community to make comparisons across studies.
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