Yu Wang

Zhilin Huang, Ling Yang, Zaixi Zhang et al.

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to capture the essential protein-ligand interactions exactly in 3D space for molecular generation. To address this problem, we propose a novel framework, namely Binding-Adaptive Diffusion Models (BindDM). In BindDM, we adaptively extract subcomplex, the essential part of binding sites responsible for protein-ligand interactions. Then the selected protein-ligand subcomplex is processed with SE(3)-equivariant neural networks, and transmitted back to each atom of the complex for augmenting the target-aware 3D molecule diffusion generation with binding interaction information. We iterate this hierarchical complex-subcomplex process with cross-hierarchy interaction node for adequately fusing global binding context between the complex and its corresponding subcomplex. Empirical studies on the CrossDocked2020 dataset show BindDM can generate molecules with more realistic 3D structures and higher binding affinities towards the protein targets, with up to -5.92 Avg. Vina Score, while maintaining proper molecular properties. Our code is available at https://github.com/YangLing0818/BindDM

Yifei Jia, Shiyu Cheng, Yu Dong et al.

Understanding the complex combustion dynamics within scramjet engines is critical for advancing high-speed propulsion technologies. However, the large scale and high dimensionality of simulation-generated temporal flow field data present significant challenges for visual interpretation, feature differentiation, and cross-case comparison. In this paper, we present TemporalFlowViz, a parameter-aware visual analytics workflow and system designed to support expert-driven clustering, visualization, and interpretation of temporal flow fields from scramjet combustion simulations. Our approach leverages hundreds of simulated combustion cases with varying initial conditions, each producing time-sequenced flow field images. We use pretrained Vision Transformers to extract high-dimensional embeddings from these frames, apply dimensionality reduction and density-based clustering to uncover latent combustion modes, and construct temporal trajectories in the embedding space to track the evolution of each simulation over time. To bridge the gap between latent representations and expert reasoning, domain specialists annotate representative cluster centroids with descriptive labels. These annotations are used as contextual prompts for a vision-language model, which generates natural-language summaries for individual frames and full simulation cases. The system also supports parameter-based filtering, similarity-based case retrieval, and coordinated multi-view exploration to facilitate in-depth analysis. We demonstrate the effectiveness of TemporalFlowViz through two expert-informed case studies and expert feedback, showing TemporalFlowViz enhances hypothesis generation, supports interpretable pattern discovery, and enhances knowledge discovery in large-scale scramjet combustion analysis.