Yifan Zhang

Lilin Fan, Xuqing Chai, Zhixiong Tian et al.

Analysis of the genome sequence of Perccottus glenii, the only fish known to possess freeze tolerance, holds significant importance for understanding how organisms adapt to extreme environments, Traditional biological analysis methods are time-consuming and have limited accuracy, To address these issues, we will employ machine learning techniques to analyze the gene sequences of Perccottus glenii, with Neodontobutis hainanens as a comparative group, Firstly, we have proposed five gene sequence vectorization methods and a method for handling ultra-long gene sequences, We conducted a comparative study on the three vectorization methods: ordinal encoding, One-Hot encoding, and K-mer encoding, to identify the optimal encoding method, Secondly, we constructed four classification models: Random Forest, LightGBM, XGBoost, and Decision Tree, The dataset used by these classification models was extracted from the National Center for Biotechnology Information database, and we vectorized the sequence matrices using the optimal encoding method, K-mer, The Random Forest model, which is the optimal model, achieved a classification accuracy of up to 99, 98 , Lastly, we utilized SHAP values to conduct an interpretable analysis of the optimal classification model, Through ten-fold cross-validation and the AUC metric, we identified the top 10 features that contribute the most to the model's classification accuracy, This demonstrates that machine learning methods can effectively replace traditional manual analysis in identifying genes associated with the freeze tolerance phenotype in Perccottus glenii.

Haoyu Zhang, Wentao Zhang, Hao Miao et al.

Spatio-Temporal Graph Neural Networks (STGNNs) have emerged as a powerful tool for modeling dynamic graph-structured data across diverse domains. However, they often fail to generalize in Spatio-Temporal Out-of-Distribution (STOOD) scenarios, where both temporal dynamics and spatial structures evolve beyond the training distribution. To address this problem, we propose an innovative Spatio-Temporal Retrieval-Augmented Pattern Learning framework,STRAP, which enhances model generalization by integrating retrieval-augmented learning into the STGNN continue learning pipeline. The core of STRAP is a compact and expressive pattern library that stores representative spatio-temporal patterns enriched with historical, structural, and semantic information, which is obtained and optimized during the training phase. During inference, STRAP retrieves relevant patterns from this library based on similarity to the current input and injects them into the model via a plug-and-play prompting mechanism. This not only strengthens spatio-temporal representations but also mitigates catastrophic forgetting. Moreover, STRAP introduces a knowledge-balancing objective to harmonize new information with retrieved knowledge. Extensive experiments across multiple real-world streaming graph datasets show that STRAP consistently outperforms state-of-the-art STGNN baselines on STOOD tasks, demonstrating its robustness, adaptability, and strong generalization capability without task-specific fine-tuning.