HELM-BERT: Topology-Aware Representations for Chemically Modified Peptides

Overview

Student talk at the 18th CBI Wakate-no-Kai Seminar (第18回 CBI若手の会講演会) on HELM-BERT, an encoder-only transformer pretrained on HELM notation for cyclic peptide membrane permeability and peptide–protein interaction prediction, as published in Journal of Chemical Information and Modeling. This presentation received the Excellent Lecture Award (優秀講演賞).

Session: 学生発表５ (14:55–15:20)

Affiliation: Kyoto University Graduate School of Medicine, Department of Biomedical Data Intelligence