SUPERMAGO: Protein Function Prediction Based on Transformer Embeddings

Recent technological advancements have enabled the experimental determination of amino acid sequences for numerous proteins. However, analyzing protein functions, which is essential for understanding their roles within cells, remains a challenging task due to the associated costs and time constraints. To address this challenge, various computational approaches have been proposed to aid in the categorization of protein functions, mainly utilizing amino acid sequences. In this study, we introduce SUPERMAGO, a method that leverages amino acid sequences to predict protein functions. Our approach employs Transformer architectures, pre-trained on protein data, to extract features from the sequences. We use multilayer perceptrons for classification and a stacking neural network to aggregate the predictions, which significantly enhances the performance of our method. We also present SUPERMAGO+, an ensemble of SUPERMAGO and DIAMOND, based on neural networks that assign different weights to each term, offering a novel weighting mechanism compared with existing methods in the literature. Additionally, we introduce SUPERMAGO+Web, a web server-compatible version of SUPERMAGO+ designed to operate with reduced computational resources. Both SUPERMAGO and SUPERMAGO+ consistently outperformed state-of-the-art approaches in our evaluations, establishing them as leading methods for this task when considering only amino acid sequence information.