The DS 2025 constitutes the proceedings of the 28th International Conference on Discovery Science, DS 2025, which took place in Ljubljana, Slovenia, during September 22-26, 2025. The 38 full papers presented in this volume were carefully reviewed and selected from 86 submissions. They were organized in topical sections as follows: the development and analysis of methods for discovering scientific knowledge, coming from machine learning, data mining, and intelligent data analysis, and big data analytics, as well as their application in various domains.