How the technologies behind self‐driving cars, social networks, ChatGPT, and DALL‐E2 are changing structural biology

M Bochtler - BioEssays, 2025 - Wiley Online Library
The performance of deep Neural Networks (NNs) in the text (ChatGPT) and image (DALL‐
E2) domains has attracted worldwide attention. Convolutional NNs (CNNs), Large …

PG-LBO: Enhancing High-Dimensional Bayesian Optimization with Pseudo-Label and Gaussian Process Guidance

T Chen, Y Duan, D Li, L Qi, Y Shi, Y Gao - Proceedings of the AAAI …, 2024 - ojs.aaai.org
Variational Autoencoder based Bayesian Optimization (VAE-BO) has demonstrated its
excellent performance in addressing high-dimensional structured optimization problems …

BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding

X Tang, X Ye, F Wu, D Shao, Y Fang, S Chen, D Xu… - bioRxiv, 2024 - biorxiv.org
Inverse protein folding, which aims to design amino acid sequences for desired protein
structures, is fundamental to protein engineering and therapeutic development. While recent …

Antibody Design with Constrained Bayesian Optimization

Y Zeng, H Elliott, P Maffettone, P Greenside… - ICLR 2024 Workshop on … - openreview.net
In therapeutic antibody design, achieving a balance between optimizing binding affinity
subject to multiple constraints, and sequence diversity within a batch for experimental …