Bing Yang

Zhan Chen, Sicheng Li, Bing Yang et al.

Graph convolutional networks have been widely used for skeleton-based action recognition due to their excellent modeling ability of non-Euclidean data. As the graph convolution is a local operation, it can only utilize the short-range joint dependencies and short-term trajectory but fails to directly model the distant joints relations and long-range temporal information that are vital to distinguishing various actions. To solve this problem, we present a multi-scale spatial graph convolution (MS-GC) module and a multi-scale temporal graph convolution (MT-GC) module to enrich the receptive field of the model in spatial and temporal dimensions. Concretely, the MS-GC and MT-GC modules decompose the corresponding local graph convolution into a set of sub-graph convolution, forming a hierarchical residual architecture. Without introducing additional parameters, the features will be processed with a series of sub-graph convolutions, and each node could complete multiple spatial and temporal aggregations with its neighborhoods. The final equivalent receptive field is accordingly enlarged, which is capable of capturing both short- and long-range dependencies in spatial and temporal domains. By coupling these two modules as a basic block, we further propose a multi-scale spatial temporal graph convolutional network (MST-GCN), which stacks multiple blocks to learn effective motion representations for action recognition. The proposed MST-GCN achieves remarkable performance on three challenging benchmark datasets, NTU RGB+D, NTU-120 RGB+D and Kinetics-Skeleton, for skeleton-based action recognition.

Yining Wang, Xumeng Gong, Shaochuan Li et al.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.