Improved Graph-Based Antibody-Aware Epitope Prediction with Protein Language Model-Based Embeddings

Abstract The accurate identification of B-cell epitopes is critical in antibody design, diagnostics, and immunotherapies. Many in silico approaches have recently been proposed to predict epitopes, but these approaches struggle primarily because of the variational and conformational nature of epitopes. However, deep learning-based approaches have recently shown great promise in achieving better performance at the epitope prediction task. In this paper, we employ a graph convolutional network (GCN) coupled with pre-trained protein language model (PLM)-based embeddings for epitope prediction on a benchmark antibody-specific epitope prediction (AsEP) dataset. We explore the use of different PLM-embedding methods on the epitope prediction task and show that the choice of PLM embeddings impacts the performance. Specifically, we find that antibody-specific PLMs such as AntiBERTy and general PLMs such as ProtTrans and ESM-2 for antigens provide improved epitope prediction performance with an AUCROC of 0.65, precision of 0.28, and recall of 0.46. The source code is available at: https://github.com/mansoor181/walle-pp.git. Competing Interest Statement The authors have declared no competing interest. Footnotes imdad.khan{at}lums.edu.pk sa4559{at}columbia.edu mahmed76{at}student.gsu.edu,ajan3{at}student.gsu.edu, mpatterson30{at}gsu.edu The bibliography and related work sections were revised with an overall reduction in the number of pages.