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arXiv · 2508.12575

Deep Learning Model for Amyloidogenicity Prediction using a Pre-trained Protein LLM

Zohra Yagoub·Hafida Bouziane
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Abstract

The prediction of amyloidogenicity in peptides and proteins remains a focal point of ongoing bioinformatics. The crucial step in this field is to apply advanced computational methodologies. Many recent approaches to predicting amyloidogenicity within proteins are highly based on evolutionary motifs and the individual properties of amino acids. It is becoming increasingly evident that the sequence information-based features show high predictive performance. Consequently, our study evaluated the contextual features of protein sequences obtained from a pretrained protein large language model leveraging bidirectional LSTM and GRU to predict amyloidogenic regions in peptide and protein sequences. Our method achieved an accuracy of 84.5% on 10-fold cross-validation and an accuracy of 83% in the test dataset. Our results demonstrate competitive performance, highlighting the potential of LLMs in enhancing the accuracy of amyloid prediction.

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Zohra Yagoub, Hafida Bouziane. 2025-08-18. Deep Learning Model for Amyloidogenicity Prediction using a Pre-trained Protein LLM. https://doi.org/10.2991/978-94-6463-805-9_22

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