We introduce DisProtEdit, a controllable protein editing framework that leverages dual-channel natural language supervision to learn disentangled representations of structural and functional properties. Unlike prior approaches that rely on joint holistic embeddings, DisProtEdit explicitly separates semantic factors, enabling modular and interpretable control. To support this, we construct SwissProtDis, a large-scale multimodal dataset where each protein sequence is paired with two textual descriptions, one for structure and one for function, automatically decomposed using a large language model. DisProtEdit aligns protein and text embeddings using alignment and uniformity objectives, while a disentanglement loss promotes independence between structural and functional semantics. At inference time, protein editing is performed by modifying one or both text inputs and decoding from the updated latent representation. Experiments on protein editing and representation learning benchmarks demonstrate that DisProtEdit performs competitively with existing methods while providing improved interpretability and controllability. On a newly constructed multi-attribute editing benchmark, the model achieves a both-hit success rate of up to 61.7%, highlighting its effectiveness in coordinating simultaneous structural and functional edits.

Masked image modeling (MIM) has become a prevalent pre-training setup for vision foundation models and attains promising performance. Despite its success, existing MIM methods discard the decoder network during downstream applica- tions, resulting in inconsistent representations between pre-training and fine-tuning and can hamper downstream task performance. In this paper, we propose a new architecture, RevColV2, which tackles this issue by keeping the entire autoen- coder architecture during both pre-training and fine-tuning. The main body of RevColV2 contains bottom-up columns and top-down columns, between which information is reversibly propagated and gradually disentangled. Such design enables our architecture with the nice property: maintaining disentangled low-level and semantic information at the end of the network in MIM pre-training.