Lei Huang

Shania Mitra, Lei Huang, Manolis Kellis

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Ze Zhang, Enyuan Zhao, Di Niu et al.

Driven by practical demands in land resource monitoring and national defense security, this paper introduces the Remote Sensing Copy-Move Question Answering (RSCMQA) task. Unlike traditional Remote Sensing Visual Question Answering (RSVQA), RSCMQA focuses on interpreting complex tampering scenarios and inferring relationships between objects. We present a suite of global RSCMQA datasets, comprising images from 29 different regions across 14 countries. Specifically, we propose five distinct datasets, including the basic dataset RS-CMQA, the category-balanced dataset RS-CMQA-B, the high-authenticity dataset Real-RSCM, the extended dataset RS-TQA, and the extended category-balanced dataset RS-TQA-B. These datasets fill a critical gap in the field while ensuring comprehensiveness, balance, and challenge. Furthermore, we introduce a region-discrimination-guided multimodal copy-move forgery perception framework (CMFPF), which enhances the accuracy of answering questions about tampered images by leveraging prompt about the differences and connections between the source and tampered domains. Extensive experiments demonstrate that our method provides a stronger benchmark for RSCMQA compared to general VQA and RSVQA models. Our datasets and code are publicly available at https://github.com/shenyedepisa/RSCMQA.

Haoran Zhao, Tong Bai, Lei Huang et al.

Diffusion models manifest evident benefits across diverse domains, yet their high sampling cost, requiring dozens of sequential model evaluations, remains a major limitation. Prior efforts mainly accelerate sampling via optimized solvers or distillation, which treat each query independently. In contrast, we reduce total number of steps by sharing early-stage sampling across semantically similar queries. To enable such efficiency gains without sacrificing quality, we propose SAGE, a semantic-aware shared sampling framework that integrates a shared sampling scheme for efficiency and a tailored training strategy for quality preservation. Extensive experiments show that SAGE reduces sampling cost by 25.5%, while improving generation quality with 5.0% lower FID, 5.4% higher CLIP, and 160% higher diversity over baselines.