Jian Liu

Alex Morehead, Xiao Chen, Tianqi Wu et al.

Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a notable influence on the biological function of the complex, computational methods that can quickly and effectively be used to refine and assess the quality of a protein complex's 3D structure can directly be used within a drug discovery pipeline to accelerate the development of new therapeutics and improve the efficacy of future vaccines. In this work, we introduce the Equivariant Graph Refiner (EGR), a novel E(3)-equivariant graph neural network (GNN) for multi-task structure refinement and assessment of protein complexes. Our experiments on new, diverse protein complex datasets, all of which we make publicly available in this work, demonstrate the state-of-the-art effectiveness of EGR for atomistic refinement and assessment of protein complexes and outline directions for future work in the field. In doing so, we establish a baseline for future studies in macromolecular refinement and structure analysis.

Xuekang Zhu, Ji-Zhe Zhou, Kaiwen Feng et al.

Image manipulations often entail a complex manipulation process, comprising a series of editing operations to create a deceptive image, exhibiting sequentiality and hierarchical characteristics. However, existing IML methods remain manipulation-process-agnostic, directly producing localization masks in a one-shot prediction paradigm without modeling the underlying editing steps. This one-shot paradigm compresses the high-dimensional compositional space into a single binary mask, inducing severe dimensional collapse, thereby creating a fundamental mismatch with the intrinsic nature of the IML task. To address this, we are the first to reformulate image manipulation localization as a conditional sequence prediction task, proposing the RITA framework. RITA predicts manipulated regions layer-by-layer in an ordered manner, using each step's prediction as the condition for the next, thereby explicitly modeling temporal dependencies and hierarchical structures among editing operations. To enable training and evaluation, we synthesize multi-step manipulation data and construct a new benchmark HSIM. We further propose the HSS metric to assess sequential order and hierarchical alignment. Extensive experiments show RITA achieves SOTA on traditional benchmarks and provides a solid foundation for the novel hierarchical localization task, validating its potential as a general and effective paradigm. The code and dataset will be publicly available.