Protein inverse folding aims to recover amino acid sequences for a given 3D protein structure, underpinning broad applications such as enzyme engineering and drug discovery.Current methods often follow a serial pipeline, in which a structure encoder predicts a coarse sequence, which is then refined by protein language models (PLMs). However, because PLMs only perform post-hoc sequence edits, the refinement is bounded by the quality of upstream predictions.Thanks to recent multimodal protein language models (MPLMs), we could directly encode structure to generate sequences with pretrained structural knowledge, but we observe that they are not effective for inverse folding. Therefore, we introduce a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.Through extensive experiments across standard protein inverse folding benchmarks, our method achieves state-of-the-art performance, surpassing prior approaches, and ablation studies validate the rationale of our symmetric design, revealing a promising direction for the community.
Han-Dong Wang, Jiaxin Qi, Baisheng Lai et al.· 0 citations
As Large Vision-Language Models increasingly aim to integrate visual generation and understanding within a single parameter space, evaluating such structural unification in a cohesive manner remains a critical challenge. Current evaluation protocols predominantly treat generative and discriminative capabilities as separate tasks, leaving a gap in system-level evaluation for unified multimodal models (UMMs). In this work, we propose Self-Generative-Understanding (SGU), a novel, annotation-free evaluation framework that probes the integrated capabilities of unified models through a semantic closed-loop challenge. Without requiring new annotations, SGU leverages the dual understanding-and-generation abilities of UMMs by asking them to first perceive an image and produce a textual description, subsequently reconstruct a visual context based on that description, and finally perform reasoning over the self-generated output. This pipeline provides a zero-cost testbed that yields an integrated performance score specifically tailored for evaluating UMMs as unified systems. Extensive experiments show that even high-performing UMMs often struggle to reason over their own generated contexts, revealing limitations that are not captured by separate evaluations of understanding or generation alone. Our work provides a complementary holistic evaluation framework and offers a foundation for benchmarking the development of next-generation unified multimodal models.
Hao Zhang, Jiaxin Qi, Zhijiang Tang et al.· 0 citations