arXiv:2508.07345cs.LGcs.AI2025-08

用图像编码提升噬菌体结构蛋白分类准确率,还能评估预测可信度。

ProteoKnight: Convolution-based Phage Virion Protein Classification and Uncertainty Analysis

  • 将蛋白质序列转为图像,用卷积网络分类
  • 二分类准确率达90.8%,优于传统方法
  • 可识别低置信度预测,适合生物实验验证

准确预测噬菌体衣壳蛋白(PVP)对基因组研究至关重要。现有计算工具依赖机器学习进行高通量测序的蛋白注释,但需特殊序列编码。本文提出ProteoKnight,基于图像编码的新方法,克服传统技术的空间信息损失问题,利用预训练卷积神经网络实现高效分类。通过蒙特卡洛丢弃法评估二分类中的预测不确定性。实验显示,二分类准确率达90.8%,性能媲美当前最优方法;多分类仍不理想。不确定性分析揭示预测置信度受蛋白类别和序列长度影响。该方法优于频率混沌游戏表示法(FCGR),在保证分类准确性的同时,可识别低置信度预测结果。

原文摘要 · Abstract (English)

\textbf{Introduction:} Accurate prediction of Phage Virion Proteins (PVP) is essential for genomic studies due to their crucial role as structural elements in bacteriophages. Computational tools, particularly machine learning, have emerged for annotating phage protein sequences from high-throughput sequencing. However, effective annotation requires specialized sequence encodings. Our paper introduces ProteoKnight, a new image-based encoding method that addresses spatial constraints in existing techniques, yielding competitive performance in PVP classification using pre-trained convolutional neural networks. Additionally, our study evaluates prediction uncertainty in binary PVP classification through Monte Carlo Dropout (MCD). \textbf{Methods:} ProteoKnight adapts the classical DNA-Walk algorithm for protein sequences, incorporating pixel colors and adjusting walk distances to capture intricate protein features. Encoded sequences were classified using multiple pre-trained CNNs. Variance and entropy measures assessed prediction uncertainty across proteins of various classes and lengths. \textbf{Results:} Our experiments achieved 90.8% accuracy in binary classification, comparable to state-of-the-art methods. Multi-class classification accuracy remains suboptimal. Our uncertainty analysis unveils variability in prediction confidence influenced by protein class and sequence length. \textbf{Conclusions:} Our study surpasses frequency chaos game representation (FCGR) by introducing novel image encoding that mitigates spatial information loss limitations. Our classification technique yields accurate and robust PVP predictions while identifying low-confidence predictions.

蛋白质分类卷积神经网络不确定性分析噬菌体

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。