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ProteoKnight demonstrates how image-based sequence encoding can effectively address spatial constraints in protein classification using pre-trained convolutional neural networks. The study further highlights the importance of uncertainty quantification via Monte Carlo Dropout, revealing how prediction confidence varies with protein class and length. This work advances bioinformatics by integrating robust machine learning techniques to improve genomic annotation accuracy for phage virion proteins.
ProteoKnight: Convolution-based Phage Virion Protein Classification and Uncertainty Analysis
arXiv:2508.07345v2 Announce Type: replace Abstract: \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.
Abstract:\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.
Machine Learning (cs.LG); Artificial Intelligence (cs.AI)
arXiv:2508.07345 [cs.LG]
(or arXiv:2508.07345v2 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2508.07345 Focus to learn more arXiv-issued DOI via DataCite
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