An Explainable Deep Learning Model for Clathrin Protein Prediction Using a DCT-Enhanced Position-Specific Scoring Matrix.

introductionClathrin protein (CP) plays a vital role in essential cellular processes, including endocytosis and signal transduction. Dysfunctions in CP have been associated with various diseases, including neurodegenerative disorders and cancer, making it a significant focus of biomedical research.

methodsThis study introduces Pred-CLGRUs, a novel computational framework for predicting Clathrin protein using Gated Recurrent Units (GRUs). Pred-CLGRUs utilize a Position-Specific Scoring Matrix (PSSM) in conjunction with the Discrete Cosine Transform (DCT) to enhance feature extraction while reducing noise and redundancy. A potential explanation for this mismatch could be that the Average Block-PSSM feature is derived from the Position-Specific Scoring Matrix (PSSM). The proposed model is trained using four deep learning architectures: GRUs, Convolutional Neural Networks (CNNs), Long Short-Term Memory (LSTM) networks, and Deep Neural Networks (DNNs).

resultsThe PSSM-DCT input enabled GRUs to achieve 93.33% accuracy, producing a Matthews Correlation Coefficient value of 0.86. Pred-CLGRUs enabled GRUs to achieve an accuracy of 93.33%, sensitivity of 94.44%, and specificity of 92.22%, while maintaining a Matthews correlation coefficient of 0.86. DISCUSSION: We began by calculating PSSM to detect evolutionary changes. The compression method named DCT was applied within each PSSM during the second implementation step.

conclusionThe predictive performance can be significantly enhanced if the model can incorporate heterogeneous types of biological information, such as structure, evolution, and function. We plan to design a novel prediction model that combines Capsule Neural Networks (CapsNet) with DeepWalk to obtain structural features.