Yinlong Xu

Zitai Kong, Yiheng Zhu, Yinlong Xu et al.

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein sequences. However, these methods mainly focus on local or shallow residual semantics and suffer from low inference efficiency, large modeling space and high training cost. To address these challenges, we introduce ProtFlow, a fast flow matching-based protein sequence design framework that operates on embeddings derived from semantically meaningful latent space of protein language models. By compressing and smoothing the latent space, ProtFlow enhances performance while training on limited computational resources. Leveraging reflow techniques, ProtFlow enables high-quality single-step sequence generation. Additionally, we develop a joint design pipeline for the design scene of multichain proteins. We evaluate ProtFlow across diverse protein design tasks, including general peptides and long-chain proteins, antimicrobial peptides, and antibodies. Experimental results demonstrate that ProtFlow outperforms task-specific methods in these applications, underscoring its potential and broad applicability in computational protein sequence design and analysis.

Weize Liu, Yinlong Xu, Hongxia Xu et al.

Recently, large language models (LLMs) have achieved tremendous breakthroughs in the field of NLP, but still lack understanding of their internal neuron activities when processing different languages. We designed a method to convert dense LLMs into fine-grained MoE architectures, and then visually studied the multilingual activation patterns of LLMs through expert activation frequency heatmaps. Through comprehensive experiments on different model families, different model sizes, and different variants, we analyzed the similarities and differences in the internal neuron activation patterns of LLMs when processing different languages. Specifically, we investigated the distribution of high-frequency activated experts, multilingual shared experts, whether multilingual activation patterns are related to language families, and the impact of instruction tuning on activation patterns. We further explored leveraging the discovered differences in expert activation frequencies to guide sparse activation and pruning. Experimental results demonstrated that our method significantly outperformed random expert pruning and even exceeded the performance of unpruned models in some languages. Additionally, we found that configuring different pruning rates for different layers based on activation level differences could achieve better results. Our findings reveal the multilingual processing mechanisms within LLMs and utilize these insights to offer new perspectives for applications such as sparse activation and model pruning.