Wanru Zhuang

Jiale Zhao, Wanru Zhuang, Jia Song et al.

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing structure-based pre-trained models primarily focus on the residue level, i.e., alpha carbon atoms, while ignoring other atoms like side chain atoms. We argue that modeling proteins at both residue and atom levels is important since the side chain atoms can also be crucial for numerous downstream tasks, for example, molecular docking. Nevertheless, we find that naively combining residue and atom information during pre-training typically fails. We identify a key reason is the information leakage caused by the inclusion of atom structure in the input, which renders residue-level pre-training tasks trivial and results in insufficiently expressive residue representations. To address this issue, we introduce a span mask pre-training strategy on 3D protein chains to learn meaningful representations of both residues and atoms. This leads to a simple yet effective approach to learning protein representation suitable for diverse downstream tasks. Extensive experimental results on binding site prediction and function prediction tasks demonstrate our proposed pre-training approach significantly outperforms other methods. Our code will be made public.

Wanru Zhuang, Wenbo Li, Zhibin Lan et al.

Text Image Machine Translation (TIMT) aims to translate texts embedded within an image into another language. Current TIMT studies primarily focus on providing translations for all the text within an image, while neglecting to provide bounding boxes and covering limited scenarios. In this work, we extend traditional TIMT into position-aware TIMT (PATIMT), aiming to support fine-grained and layoutpreserving translation, which holds great practical value but remains largely unexplored. This task comprises two key sub-tasks: regionspecific translation and full-image translation with grounding. To support existing models on PATIMT and conduct fair evaluation, we construct the PATIMT benchmark (PATIMTBench), which consists of 10 diverse real-world scenarios. Specifically, we introduce an Adaptive Image OCR Refinement Pipeline, which adaptively selects appropriate OCR tools based on scenario and refines the results of text-rich images. To ensure evaluation reliability, we further construct a test set, which contains 1,200 high-quality instances manually annotated and reviewed by human experts. After fine-tuning on our data, compact Large Vision-Language Models (LVLMs) achieve state-of-the-art performance on both sub-tasks. Experimental results also highlight the scalability and generalizability of our training data