Mengyun Chen

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.

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.

Xingwang Li, Mengyun Chen, Jiamou Liu et al.

In the face of accelerating global urbanization and the increasing frequency of extreme weather events, highresolution urban rainfall monitoring is crucial for building resilient smart cities. Commercial Microwave Links (CMLs) are an emerging data source with great potential for this task.While traditional rainfall retrieval from CMLs relies on physicsbased models, these often struggle with real-world complexities like signal noise and nonlinear attenuation. To address these limitations, this paper proposes a novel hybrid deep learning architecture based on the Transformer and a Bidirectional Gated Recurrent Unit (BiGRU), which we name TabGRU. This design synergistically captures both long-term dependencies and local sequential features in the CML signal data. The model is further enhanced by a learnable positional embedding and an attention pooling mechanism to improve its dynamic feature extraction and generalization capabilities. The model was validated on a public benchmark dataset from Gothenburg, Sweden (June-September 2015). The evaluation used 12 sub-links from two rain gauges (Torp and Barl) over a test period (August 22-31) covering approximately 10 distinct rainfall events. The proposed TabGRU model demonstrated consistent advantages, outperforming deep learning baselines and achieving high coefficients of determination (R2) at both the Torp site (0.91) and the Barl site (0.96). Furthermore, compared to the physics-based approach, TabGRU maintained higher accuracy and was particularly effective in mitigating the significant overestimation problem observed in the PL model during peak rainfall events. This evaluation confirms that the TabGRU model can effectively overcome the limitations of traditional methods, providing a robust and accurate solution for CML-based urban rainfall monitoring under the tested conditions.

Mengyun Chen, Tao Ge, Xingxing Zhang et al.

We propose a novel language-independent approach to improve the efficiency for Grammatical Error Correction (GEC) by dividing the task into two subtasks: Erroneous Span Detection (ESD) and Erroneous Span Correction (ESC). ESD identifies grammatically incorrect text spans with an efficient sequence tagging model. Then, ESC leverages a seq2seq model to take the sentence with annotated erroneous spans as input and only outputs the corrected text for these spans. Experiments show our approach performs comparably to conventional seq2seq approaches in both English and Chinese GEC benchmarks with less than 50% time cost for inference.

Minghan Yang, Dong Xu, Hongyu Chen et al.

In this paper, we consider stochastic second-order methods for minimizing a finite summation of nonconvex functions. One important key is to find an ingenious but cheap scheme to incorporate local curvature information. Since the true Hessian matrix is often a combination of a cheap part and an expensive part, we propose a structured stochastic quasi-Newton method by using partial Hessian information as much as possible. By further exploiting either the low-rank structure or the kronecker-product properties of the quasi-Newton approximations, the computation of the quasi-Newton direction is affordable. Global convergence to stationary point and local superlinear convergence rate are established under some mild assumptions. Numerical results on logistic regression, deep autoencoder networks and deep convolutional neural networks show that our proposed method is quite competitive to the state-of-the-art methods.

Minghan Yang, Dong Xu, Zaiwen Wen et al.

In this paper, we develop an efficient sketchy empirical natural gradient method (SENG) for large-scale deep learning problems. The empirical Fisher information matrix is usually low-rank since the sampling is only practical on a small amount of data at each iteration. Although the corresponding natural gradient direction lies in a small subspace, both the computational cost and memory requirement are still not tractable due to the high dimensionality. We design randomized techniques for different neural network structures to resolve these challenges. For layers with a reasonable dimension, sketching can be performed on a regularized least squares subproblem. Otherwise, since the gradient is a vectorization of the product between two matrices, we apply sketching on the low-rank approximations of these matrices to compute the most expensive parts. A distributed version of SENG is also developed for extremely large-scale applications. Global convergence to stationary points is established under some mild assumptions and a fast linear convergence is analyzed under the neural tangent kernel (NTK) case. Extensive experiments on convolutional neural networks show the competitiveness of SENG compared with the state-of-the-art methods. On the task ResNet50 with ImageNet-1k, SENG achieves 75.9\% Top-1 testing accuracy within 41 epochs. Experiments on the distributed large-batch training show that the scaling efficiency is quite reasonable.