arXiv:2503.14574q-bio.QMcs.LG2025-03被引 1

用贝塞尔曲线将序列转为图像,提升生物序列分类效果

Sequence Analysis Using the Bezier Curve

  • 用贝塞尔曲线映射序列元素,避免传统方法像素稀疏问题
  • 在多个序列数据集上实现优异分类性能,优于现有图像化方法
  • 适合生物信息学、药物发现等需要序列分析的领域

序列分析(如蛋白质、DNA和SMILES字符串)在疾病诊断、生物材料工程、基因工程和药物发现中至关重要。传统方法将序列转化为数值表示以应用机器学习/深度学习模型,但受限于深度学习模型对表格数据表现不佳。另一类方法采用混沌游戏表示(CGR)将序列转为图像,但存在将序列元素映射到图像中少数像素的问题,导致图像稀疏,难以充分表达序列信息,影响预测效果。本研究提出一种新方法,利用贝塞尔曲线概念将序列元素映射到曲线,增强图像中的序列信息表达,从而提升深度学习分类性能。我们在多个序列数据集上验证该方法,涵盖不同分类任务,结果表明贝塞尔曲线方法在所有任务中均表现出色。

原文摘要 · Abstract (English)

The analysis of sequences (e.g., protein, DNA, and SMILES string) is essential for disease diagnosis, biomaterial engineering, genetic engineering, and drug discovery domains. Conventional analytical methods focus on transforming sequences into numerical representations for applying machine learning/deep learning-based sequence characterization. However, their efficacy is constrained by the intrinsic nature of deep learning (DL) models, which tend to exhibit suboptimal performance when applied to tabular data. An alternative group of methodologies endeavors to convert biological sequences into image forms by applying the concept of Chaos Game Representation (CGR). However, a noteworthy drawback of these methods lies in their tendency to map individual elements of the sequence onto a relatively small subset of designated pixels within the generated image. The resulting sparse image representation may not adequately encapsulate the comprehensive sequence information, potentially resulting in suboptimal predictions. In this study, we introduce a novel approach to transform sequences into images using the Bézier curve concept for element mapping. Mapping the elements onto a curve enhances the sequence information representation in the respective images, hence yielding better DL-based classification performance. We employed different sequence datasets to validate our system by using different classification tasks, and the results illustrate that our Bézier curve method is able to achieve good performance for all the tasks.

序列分析贝塞尔曲线图像化生物信息

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