Since its founding in 2001, the International Workshop on Data Mining in Bioinformatics (BIOKDD) has served as a leading forum where data mining researchers and biomedical scientists come together to tackle some of the most complex problems in biology.

From its early years alongside the Association for Computing Machinery’s Special Interest Group on Knowledge Discovery and Data Mining (ACM SIGKDD) conference to its continued growth over two decades, BIOKDD has catalyzed innovations in biomolecular network discovery, visual analytics, and AI-driven therapeutics. The 2025 edition of the workshop continued this tradition by focusing on emerging challenges such as protein foundational models and large language models for biomolecular design.

UAB’s SPARC at the helm

This year, the UAB’s SPARC center played a prominent role in organizing the event.

• Truong Son Hy, Ph.D., a SPARC member, served as program co-chair.
• Jake Y. Chen, Ph.D., SPARC director and one of BIOKDD’s original founders in 2001, took on the role of general chair.

Their leadership underscored SPARC’s mission to accelerate AI-driven systems pharmacology and translational informatics — bridging the gap between cutting-edge computational methods and practical biomedical applications.

Cutting-Edge Research

Among the highlights was a contribution from UAB’s HySonLab:

• The preprint “LANTERN: Leveraging Large Language Models and Transformers for Enhanced Molecular Interactions” by Cong Nga Ha, Phuc Pham, and Hy
• Truong Son introduced a transformer-based framework for predicting drug–target, protein–protein, and drug–drug interactions at scale.

This breakthrough offers a promising path to accelerating therapeutic discovery by harnessing the power of AI to untangle complex biological relationships.

Distinguished Keynotes

The workshop also featured talks from world-renowned experts in data mining and computational science:

• Jiawei Han, Ph.D. (University of Illinois Urbana-Champaign), is celebrated as the “grandfather of data mining” for his pioneering work in pattern mining and big-data analytics.
• Wei Wang, Ph.D. (University of California, Los Angeles), chair of the Computer Science Department and former ACM SIGKDD chair, with deep expertise in scalable analytics and bioinformatics.
• Geoffrey Charles Fox, Ph.D. (University of Georgia), a luminary in computational science and director of the Digital Science Center.

Looking Ahead

As AI methods continue to reshape biomedicine, BIOKDD remains a vital platform for collaboration between computer scientists and biomedical researchers. This year’s event not only celebrated two decades of impact but also set the stage for future breakthroughs in precision medicine, drug discovery, and systems biology.