Siyuan Li

Yufei Huang, Siyuan Li, Jin Su et al.

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community.

Xiongfei Su, Siyuan Li, Yuning Cui et al.

Image dehazing is a crucial task that involves the enhancement of degraded images to recover their sharpness and textures. While vision Transformers have exhibited impressive results in diverse dehazing tasks, their quadratic complexity and lack of dehazing priors pose significant drawbacks for real-world applications. In this paper, guided by triple priors, Bright Channel Prior (BCP), Dark Channel Prior (DCP), and Histogram Equalization (HE), we propose a \textit{P}rior-\textit{g}uided Hierarchical \textit{H}armonization Network (PGH$^2$Net) for image dehazing. PGH$^2$Net is built upon the UNet-like architecture with an efficient encoder and decoder, consisting of two module types: (1) Prior aggregation module that injects B/DCP and selects diverse contexts with gating attention. (2) Feature harmonization modules that subtract low-frequency components from spatial and channel aspects and learn more informative feature distributions to equalize the feature maps.

Jiangbin Zheng, Stan Z. Li

While deep generative models show promise for learning inverse protein folding directly from data, the lack of publicly available structure-sequence pairings limits their generalization. Previous improvements and data augmentation efforts to overcome this bottleneck have been insufficient. To further address this challenge, we propose a novel protein design paradigm called MMDesign, which leverages multi-modality transfer learning. To our knowledge, MMDesign is the first framework that combines a pretrained structural module with a pretrained contextual module, using an auto-encoder (AE) based language model to incorporate prior protein semantic knowledge. Experimental results, only training with the small dataset, demonstrate that MMDesign consistently outperforms baselines on various public benchmarks. To further assess the biological plausibility, we present systematic quantitative analysis techniques that provide interpretability and reveal more about the laws of protein design.