Bin Feng

Zijing Liu, Bin Feng, He Cao et al.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Jiayi Pan, Chengcan Wang, Kaifu Zheng et al.

Large language models (LLMs) have shown remarkable capabilities in various tasks. However their huge model size and the consequent demand for computational and memory resources also pose challenges to model deployment. Currently, 4-bit post-training quantization (PTQ) has achieved some success in LLMs, reducing the memory footprint by approximately 75% compared to FP16 models, albeit with some accuracy loss. In this paper, we propose SmoothQuant+, an accurate and efficient 4-bit weight-only PTQ that requires no additional training, which enables lossless in accuracy for LLMs for the first time. Based on the fact that the loss of weight quantization is amplified by the activation outliers, SmoothQuant+ smoothes the activation outliers by channel before quantization, while adjusting the corresponding weights for mathematical equivalence, and then performs group-wise 4-bit weight quantization for linear layers. We have integrated SmoothQuant+ into the vLLM framework, an advanced high-throughput inference engine specially developed for LLMs, and equipped it with an efficient W4A16 CUDA kernels, so that vLLM can seamlessly support SmoothQuant+ 4-bit weight quantization. Our results show that, with SmoothQuant+, the Code Llama-34B model can be quantized and deployed on a A100 40GB GPU, achieving lossless accuracy and a throughput increase of 1.9 to 4.0 times compared to the FP16 model deployed on two A100 40GB GPUs. Moreover, the latency per token is only 68% of the FP16 model deployed on two A100 40GB GPUs. This is the state-of-the-art 4-bit weight quantization for LLMs as we know.