Junde Xu

InstructPLM-mu: protein fitness prediction from structure instructions

Abstract Multimodal protein language models (PLMs) deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and investigate the question: Can a pretrained sequence-...

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling

Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives such as denoising and masked prediction. While prior studies have shown that generative models often learn suboptimal representations for unde...

CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware kcat Prediction