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.