Lijie Su

Yining Qian, Lijie Su, Meiling Xu et al.

Predicting protein secondary structure is essential for understanding protein function and advancing drug discovery. However, the intricate sequence-structure relationship poses significant challenges for accurate modeling. To address these, we propose MOGP-MMF, a multi-objective genetic programming framework that reformulates PSSP as an automated optimization task focused on feature selection and fusion. Specifically, MOGP-MMF introduces a multi-view multi-level representation strategy that integrates evolutionary, semantic, and newly introduced structural views to capture the comprehensive protein folding logic. Leveraging an enriched operator set, the framework evolves both linear and nonlinear fusion functions, effectively capturing high-order feature interactions while reducing fusion complexity. To resolve the accuracy-complexity trade-off, an improved multi-objective GP algorithm is developed, incorporating a knowledge transfer mechanism that utilizes prior evolutionary experience to guide the population toward global optima. Extensive experiments across seven benchmark datasets demonstrate that MOGP-MMF surpasses state-of-the-art methods, particularly in Q8 accuracy and structural integrity. Furthermore, MOGP-MMF generates a diverse set of non-dominated solutions, offering flexible model selection schemes for various practical application scenarios. The source code is available on GitHub: https://github.com/qian-ann/MOGP-MMF/tree/main.

Yang Yang, Tong Zhang, Jian Wu et al.

With the rapid advancement of large language models, academic topic identification and topic evolution analysis are crucial for enhancing AI's understanding capabilities. Dynamic topic analysis provides a powerful approach to capturing and understanding the temporal evolution of topics in large-scale datasets. This paper presents a two-stage dynamic topic analysis framework that incorporates convex optimization to improve topic consistency, sparsity, and interpretability. In Stage 1, a two-layer non-negative matrix factorization (NMF) model is employed to extract annual topics and identify key terms. In Stage 2, a convex optimization algorithm refines the dynamic topic structure using the convex NMF (cNMF) model, further enhancing topic integration and stability. Applying the proposed method to IEEE journal abstracts from 2004 to 2022 effectively identifies and quantifies emerging research topics, such as COVID-19 and digital twins. By optimizing sparsity differences in the clustering feature space between traditional and emerging research topics, the framework provides deeper insights into topic evolution and ranking analysis. Moreover, the NMF-cNMF model demonstrates superior stability in topic consistency. At sparsity levels of 0.4, 0.6, and 0.9, the proposed approach improves topic ranking stability by 24.51%, 56.60%, and 36.93%, respectively. The source code (to be open after publication) is available at https://github.com/meetyangyang/CDNMF.