Cheng Yang

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.

Lang Qian, Shengjie Zheng, Chunshan Deng et al.

Brain-computer interfaces (BCIs), is ways for electronic devices to communicate directly with the brain. For most medical-type brain-computer interface tasks, the activity of multiple units of neurons or local field potentials is sufficient for decoding. But for BCIs used in neuroscience research, it is important to separate out the activity of individual neurons. With the development of large-scale silicon technology and the increasing number of probe channels, artificially interpreting and labeling spikes is becoming increasingly impractical. In this paper, we propose a novel modeling framework: Adaptive Contrastive Learning Model that learns representations from spikes through contrastive learning based on the maximizing mutual information loss function as a theoretical basis. Based on the fact that data with similar features share the same labels whether they are multi-classified or binary-classified. With this theoretical support, we simplify the multi-classification problem into multiple binary-classification, improving both the accuracy and the runtime efficiency. Moreover, we also introduce a series of enhancements for the spikes, while solving the problem that the classification effect is affected because of the overlapping spikes.