Fan Xu

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.

Naifu Zhang, Meixia Tao, Jia Wang et al.

One of the main focuses in distributed learning is communication efficiency, since model aggregation at each round of training can consist of millions to billions of parameters. Several model compression methods, such as gradient quantization and sparsification, have been proposed to improve the communication efficiency of model aggregation. However, the information-theoretic minimum communication cost for a given distortion of gradient estimators is still unknown. In this paper, we study the fundamental limit of communication cost of model aggregation in distributed learning from a rate-distortion perspective. By formulating the model aggregation as a vector Gaussian CEO problem, we derive the rate region bound and sum-rate-distortion function for the model aggregation problem, which reveals the minimum communication rate at a particular gradient distortion upper bound. We also analyze the communication cost at each iteration and total communication cost based on the sum-rate-distortion function with the gradient statistics of real-world datasets. It is found that the communication gain by exploiting the correlation between worker nodes is significant for SignSGD, and a high distortion of gradient estimator can achieve low total communication cost in gradient compression.

Cheng Deng, Fan Xu, Jiaxing Ding et al.

Graph representation learning has been widely studied and demonstrated effectiveness in various graph tasks. Most existing works embed graph data in the Euclidean space, while recent works extend the embedding models to hyperbolic or spherical spaces to achieve better performance on graphs with complex structures, such as hierarchical or ring structures. Fusing the embedding from different manifolds can further take advantage of the embedding capabilities over different graph structures. However, existing embedding fusion methods mostly focus on concatenating or summing up the output embeddings, without considering interacting and aligning the embeddings of the same vertices on different manifolds, which can lead to distortion and impression in the final fusion results. Besides, it is also challenging to fuse the embeddings of the same vertices from different coordinate systems. In face of these challenges, we propose the Fused Manifold Graph Neural Network (FMGNN), a novel GNN architecture that embeds graphs into different Riemannian manifolds with interaction and alignment among these manifolds during training and fuses the vertex embeddings through the distances on different manifolds between vertices and selected landmarks, geometric coresets. Our experiments demonstrate that FMGNN yields superior performance over strong baselines on the benchmarks of node classification and link prediction tasks.

Xu Zhang, Zhifei Liu, Jiahao Wang et al. · pku

Despite the rapid advancement of large language models, they remain highly susceptible to generating hallucinations, which significantly hinders their widespread application. Hallucination research requires dynamic and fine-grained evaluation. However, most existing hallucination benchmarks (especially in Chinese language) rely on human annotations, making automatical and cost-effective hallucination evaluation challenging. To address this, we introduce HaluAgent, an agentic framework that automatically constructs fine-grained QA dataset based on some knowledge documents. Our experiments demonstrate that the manually designed rules and prompt optimization can improve the quality of generated data. Using HaluAgent, we construct C-FAITH, a Chinese QA hallucination benchmark created from 1,399 knowledge documents obtained from web scraping, totaling 60,702 entries. We comprehensively evaluate 16 mainstream LLMs with our proposed C-FAITH, providing detailed experimental results and analysis.