Peng Zhang

Mengren, Liu, Yixiang Zhang et al.

Recent advances in protein language models (PLMs) have demonstrated remarkable capabilities in understanding protein sequences. However, the extent to which different model architectures capture antibody-specific biological properties remains unexplored. In this work, we systematically investigate how architectural choices in PLMs influence their ability to comprehend antibody sequence characteristics and functions. We evaluate three state-of-the-art PLMs-AntiBERTa, BioBERT, and ESM2--against a general-purpose language model (GPT-2) baseline on antibody target specificity prediction tasks. Our results demonstrate that while all PLMs achieve high classification accuracy, they exhibit distinct biases in capturing biological features such as V gene usage, somatic hypermutation patterns, and isotype information. Through attention attribution analysis, we show that antibody-specific models like AntiBERTa naturally learn to focus on complementarity-determining regions (CDRs), while general protein models benefit significantly from explicit CDR-focused training strategies. These findings provide insights into the relationship between model architecture and biological feature extraction, offering valuable guidance for future PLM development in computational antibody design.

Yingzhanghao Zhou, Xiang Chen, Peng Zhang et al.

Since proposed in the 70s, the Non-Equilibrium Green Function (NEGF) method has been recognized as a standard approach to quantum transport simulations. Although it achieves superiority in simulation accuracy, the tremendous computational cost makes it unbearable for high-throughput simulation tasks such as sensitivity analysis, inverse design, etc. In this work, we propose AD-NEGF, to our best knowledge the first end-to-end differentiable NEGF model for quantum transport simulations. We implement the entire numerical process in PyTorch, and design customized backward pass with implicit layer techniques, which provides gradient information at an affordable cost while guaranteeing the correctness of the forward simulation. The proposed model is validated with applications in calculating differential physical quantities, empirical parameter fitting, and doping optimization, which demonstrates its capacity to accelerate the material design process by conducting gradient-based parameter optimization.