Zhengyi Li

Zhengyi Li, Kang Yang, Jin Tan et al.

Transformer models have gained significant attention due to their power in machine learning tasks. Their extensive deployment has raised concerns about the potential leakage of sensitive information during inference. However, when being applied to Transformers, existing approaches based on secure two-party computation (2PC) bring about efficiency limitations in two folds: (1) resource-intensive matrix multiplications in linear layers, and (2) complex non-linear activation functions like $\mathsf{GELU}$ and $\mathsf{Softmax}$. This work presents a new two-party inference framework $\mathsf{Nimbus}$ for Transformer models. For the linear layer, we propose a new 2PC paradigm along with an encoding approach to securely compute matrix multiplications based on an outer-product insight, which achieves $2.9\times \sim 12.5\times$ performance improvements compared to the state-of-the-art (SOTA) protocol. For the non-linear layer, through a new observation of utilizing the input distribution, we propose an approach of low-degree polynomial approximation for $\mathsf{GELU}$ and $\mathsf{Softmax}$, which improves the performance of the SOTA polynomial approximation by $2.9\times \sim 4.0\times$, where the average accuracy loss of our approach is 0.08\% compared to the non-2PC inference without privacy. Compared with the SOTA two-party inference, $\mathsf{Nimbus}$ improves the end-to-end performance of \bert{} inference by $2.7\times \sim 4.7\times$ across different network settings.

Zhengyi Li, Menglu Li, Lida Zhu et al.

Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom granularity. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, multigranularity structure-aware representation learning is designed to learn neighborhood structure representations at the amino acid, atom, and whole protein granularity from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations.Additionally, multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of PTM sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods.