Yu Fan

Sirui Liu, Jun Zhang, Haotian Chu et al.

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. To the best of our knowledge, the existing open source datasets are far less to satisfy the needs of modern protein sequence-structure related research. To solve this problem, we present the first million-level protein structure prediction dataset with high coverage and diversity, named as PSP. This dataset consists of 570k true structure sequences (10TB) and 745k complementary distillation sequences (15TB). We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset. We validate the utility of this dataset for training by participating CAMEO contest in which our model won the first place. We hope our PSP dataset together with the training benchmark can enable a broader community of AI/biology researchers for AI-driven protein related research.

Yu Fan, Zicheng Zhang, Wei Sun et al.

Point cloud is one of the most widely used digital formats of 3D models, the visual quality of which is quite sensitive to distortions such as downsampling, noise, and compression. To tackle the challenge of point cloud quality assessment (PCQA) in scenarios where reference is not available, we propose a no-reference quality assessment metric for colored point cloud based on captured video sequences. Specifically, three video sequences are obtained by rotating the camera around the point cloud through three specific orbits. The video sequences not only contain the static views but also include the multi-frame temporal information, which greatly helps understand the human perception of the point clouds. Then we modify the ResNet3D as the feature extraction model to learn the correlation between the capture videos and corresponding subjective quality scores. The experimental results show that our method outperforms most of the state-of-the-art full-reference and no-reference PCQA metrics, which validates the effectiveness of the proposed method.

Jun Zhang, Sirui Liu, Mengyun Chen et al.

Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and medical development. Determining accurate folding landscape using co-evolutionary information is fundamental to the success of modern protein structure prediction methods. As the state of the art, AlphaFold2 has dramatically raised the accuracy without performing explicit co-evolutionary analysis. Nevertheless, its performance still shows strong dependence on available sequence homologs. Based on the interrogation on the cause of such dependence, we presented EvoGen, a meta generative model, to remedy the underperformance of AlphaFold2 for poor MSA targets. By prompting the model with calibrated or virtually generated homologue sequences, EvoGen helps AlphaFold2 fold accurately in low-data regime and even achieve encouraging performance with single-sequence predictions. Being able to make accurate predictions with few-shot MSA not only generalizes AlphaFold2 better for orphan sequences, but also democratizes its use for high-throughput applications. Besides, EvoGen combined with AlphaFold2 yields a probabilistic structure generation method which could explore alternative conformations of protein sequences, and the task-aware differentiable algorithm for sequence generation will benefit other related tasks including protein design.

Zhiyuan Fang, Yuegui Huang, Zicong Hong et al.

Mixture of Experts (MoE), with its distinctive sparse structure, enables the scaling of language models up to trillions of parameters without significantly increasing computational costs. However, the substantial parameter size presents a challenge for inference, as the expansion in GPU memory cannot keep pace with the growth in parameters. Although offloading techniques utilise memory from the CPU and disk and parallelise the I/O and computation for efficiency, the computation for each expert in MoE models is often less than the I/O, resulting in numerous bubbles in the pipeline. Therefore, we propose Klotski, an efficient MoE inference engine that significantly reduces pipeline bubbles through a novel expert-aware multi-batch pipeline paradigm. The proposed paradigm uses batch processing to extend the computation time of the current layer to overlap with the loading time of the next layer. Although this idea has been effectively applied to dense models, more batches may activate more experts in the MoE, leading to longer loading times and more bubbles. Thus, unlike traditional approaches, we balance computation and I/O time and minimise bubbles by orchestrating their inference orders based on their heterogeneous computation and I/O requirements and activation patterns under different batch numbers. Moreover, to adapt to different hardware environments and models, we design a constraint-sensitive I/O-compute planner and a correlation-aware expert prefetcher for a schedule that minimises pipeline bubbles. Experimental results demonstrate that Klotski achieves a superior throughput-latency trade-off compared to state-of-the-art techniques, with throughput improvements of up to 85.12x.

Zhiyuan Fang, Zicong Hong, Yuegui Huang et al.

Large Language Models (LLMs) have demonstrated impressive performance across various tasks, and their application in edge scenarios has attracted significant attention. However, sparse-activated Mixture-of-Experts (MoE) models, which are well suited for edge scenarios, have received relatively little attention due to their high memory demands. Offload-based methods have been proposed to address this challenge, but they face difficulties with expert prediction. Inaccurate expert predictions can result in prolonged inference delays. To promote the application of MoE models in edge scenarios, we propose Fate, an offloading system designed for MoE models to enable efficient inference in resource-constrained environments. The key insight behind Fate is that gate inputs from adjacent layers can be effectively used for expert prefetching, achieving high prediction accuracy without additional GPU overhead. Furthermore, Fate employs a shallow-favoring expert caching strategy that increases the expert hit rate to 99\%. Additionally, Fate integrates tailored quantization strategies for cache optimization and IO efficiency. Experimental results show that, compared to Load on Demand and Expert Activation Path-based method, Fate achieves up to 4.5x and 1.9x speedups in prefill speed and up to 4.1x and 2.2x speedups in decoding speed, respectively, while maintaining inference quality. Moreover, Fate's performance improvements are scalable across different memory budgets.