An omics-driven computational model for angiogenic protein prediction: Advancing therapeutic strategies with Ens-deep-AGP

Angiogenic proteins (AGPs) play a critical role in both pathological and physiological activities, making them key therapeutic targets in diseases like cancer, heart disease, and stroke. Traditional methods for identifying AGPs are labor-intensive and time-consuming, creating a need for more efficient approaches. This study addresses this challenge by developing a novel computational model, Ens-Deep-AGP, designed to enhance AGP prediction. The model introduces innovative feature engineering techniques, including Position Specific Scoring Matrix-Decomposition-Discrete Cosine Transform (PSSM-DC-DCT) and Position Specific Scoring Matrix-Auto-Cross-Discrete Wavelet Transform (PSSM-ACC-DWT), which capture comprehensive protein sequence information. The ensemble feature set of these approaches are then fed into Multi-headed Ensemble Residual Convolutional Neural Network (MERCNN), a robust deep learning architecture. Ens-Deep-AGP achieved remarkable accuracy rates of 99.79 % on training dataset and 92.97 % on testing dataset, surpassing Convolutional Neural Networks (CNN), Gated Recurrent Units (GRU), and Bidirectional Long Short-Term Memory Networks (BiLSTM). The successful prediction of AGPs is crucial for accelerating drug development, discovering novel therapeutic targets and deepen our understanding of AGPs' complex roles in healthcare.