The two-volume set LNAI 15875 + 15876 constitutes the proceedings of the 29th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2025 Special Session, held in Sydney, NSW, Australia, during June 10–13, 2025. The 68 full papers included in this set were carefully reviewed and selected from 696 submissions. They were organized in topical sections as follows: survey track; machine learning; trustworthiness; learning on complex data; graph mining; machine learning applications; representation learning; scientific/business data analysis; and special track on large language models.