Multi-objective Genetic Programming with Multi-view Multi-level Feature for Enhanced Protein Secondary Structure Prediction

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.

A Novel Black Box Process Quality Optimization Approach based on Hit Rate

Hit rate is a key performance metric in predicting process product quality in integrated industrial processes. It represents the percentage of products accepted by downstream processes within a controlled range of quality. However, optimizing hit rate is a non-convex and challenging problem. To address this issue, we propose a data-driven quasi-convex approach that combines factorial hidden Markov models, multitask elastic net, and quasi-convex optimization. Our approach converts the original non-convex problem into a set of convex feasible problems, achieving an optimal hit rate. We verify the convex optimization property and quasi-convex frontier through Monte Carlo simulations and real-world experiments in steel production. Results demonstrate that our approach outperforms classical models, improving hit rates by at least 41.11% and 31.01% on two real datasets. Furthermore, the quasi-convex frontier provides a reference explanation and visualization for the deterioration of solutions obtained by conventional models.