arXiv:2412.20616cs.LGq-bio.OT2024-12

用希尔伯特曲线将分子序列转为图像,提升深度学习分类效果

Hilbert Curve Based Molecular Sequence Analysis

  • 基于希尔伯特曲线构建字母索引映射,生成序列图像表示
  • 在肺癌数据集上达94.5%准确率和93.9%F1值,优于现有方法
  • 适用于各类分子序列,可对接主流视觉模型,适合生物信息研究者

精准的分子序列分析是生物信息学中的关键任务。为应用序列分类算法,需生成合适的序列表示。传统数值化方法多依赖序列比对,存在精度不足问题;虽已有无比对技术,但其表格形式在深度学习模型中表现不佳,远逊于图像数据。为此,本文提出一种通用的希尔伯特曲线基混沌游戏表示(CGR)方法,通过创新的字母索引映射技术,将分子序列转换为希尔伯特曲线图像表示。该方法可广泛应用于任意分子序列数据,生成的图像可作为复杂视觉深度学习模型的输入。实验表明,该方法在肺部癌症数据集上使用CNN模型时,达到94.5%的准确率与93.9%的F1分数,显著优于当前最优方法,为利用图像分类技术探索分子序列分析开辟了新路径。

原文摘要 · Abstract (English)

Accurate molecular sequence analysis is a key task in the field of bioinformatics. To apply molecular sequence classification algorithms, we first need to generate the appropriate representations of the sequences. Traditional numeric sequence representation techniques are mostly based on sequence alignment that faces limitations in the form of lack of accuracy. Although several alignment-free techniques have also been introduced, their tabular data form results in low performance when used with Deep Learning (DL) models compared to the competitive performance observed in the case of image-based data. To find a solution to this problem and to make Deep Learning (DL) models function to their maximum potential while capturing the important spatial information in the sequence data, we propose a universal Hibert curve-based Chaos Game Representation (CGR) method. This method is a transformative function that involves a novel Alphabetic index mapping technique used in constructing Hilbert curve-based image representation from molecular sequences. Our method can be globally applied to any type of molecular sequence data. The Hilbert curve-based image representations can be used as input to sophisticated vision DL models for sequence classification. The proposed method shows promising results as it outperforms current state-of-the-art methods by achieving a high accuracy of $94.5$\% and an F1 score of $93.9\%$ when tested with the CNN model on the lung cancer dataset. This approach opens up a new horizon for exploring molecular sequence analysis using image classification methods.

分子序列图像化深度学习希尔伯特曲线

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