Detailed Program
Workshop Time: Monday, Aug 10, 2026, 8:00 AM - 5:30 PM (KST, UTC+9)
Workshop Room: 401A
Workshop Host: Zongliang Yue (Auburn University)
Zoom Link: https://auburn.zoom.us/j/2055634481
Poster Display Location: ICC 1 - Foyer between Halla and Samda Hall
| 8:00 AM - 8:15 AM |
Opening: The Review of 25-Year History of BIOKDD and the Future of AI, Systems Biology, and Digital Twins in Biomedical Discovery Prof. Jake Chen |
Session 1: Digital Twins and Precision Medicine (8:15 AM - 9:30 AM)
| 8:15 AM - 8:30 AM |
7. Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations Dongmin Bang, Sugyun An, Inyoung Sung, Ilho Yun, Sun Kim and Sangseon Lee |
| 8:30 AM - 8:45 AM |
10. SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing Chen Zhu, Shuyu Chen, Ye Zhang, Yang Li, Qiqi Xie and Haohan Wang |
| 8:45 AM - 9:00 AM |
15. A Time-to-Event Digital Twin Framework for Predicting ALS Progression and Healthcare Utilization Zongliang Yue, Qi Li, Terry Heiman-Patterson, Frank Bearoff, Zhaohui Qin, and Huanmei Wu |
| 9:00 AM – 9:15 AM |
18. RiboRep: Replicate-Aware Cross-Modal Transformers for Codon-Resolved Ribosome Density Prediction Ai-te Kuo, Zongliang Yue, Wei-Shinn Ku and Hao Chen |
| 9:15 AM – 9:30 AM |
21. Toward Digital Twin-Ready Brain Tumor Segmentation: A Multi-Pillar Comparison of Transformer and Convolutional Models Tanmoy Debnath and Miroslaw Narbutt |
Coffee Break (9:30 AM - 10:00 AM)
Session 2: AI for Functional Genomics and Biological Knowledge Discovery (10:00 AM - 10:45 AM)
| 10:00 AM – 10:15 AM |
2. PlantBGC: Transformer for Plant BGC Discovery via Label-Free Domain Adaptation and Weak Supervision Yuhan Zhao, Nidhi Grover, Zhishan Guo and Ning Sui |
| 10:15 AM – 10:30 AM |
6. LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology Ximing Ran, Jie Xu, Peng Jin, Zhaohui Qin, Zhexing Wen, and Jiaying Lu |
| 10:30 AM - 10:45 AM |
5. MolDeBERTa: Foundational Model for Physicochemical and Substructure-Informed Molecular Representation Learning Gabriel Bianchin de Oliveira and Fahad Saeed |
Session 3: Protein Structure and Representation Learning (10:45 AM - 11:45 AM)
| 10:45 AM – 11:00 AM |
11. Stability-Informed Low-N Learning of Protein Fitness Landscape Shannon Zhang and Yunan Luo |
| 11:00 AM – 11:15 AM |
13. PRIME: Protein Representation via Physics-Informed Multiscale Equivariant Hierarchies Viet Thanh Duy Nguyen, John K. Johnstone and Truong-Son Hy |
| 11:15 AM – 11:30 AM |
14. Geometry-Informed Parameter-Efficient Fine-Tuning of Pre-trained Molecular GNNs for Blood-Brain Barrier Permeability Prediction Marco Vega, Long Nguyen and Binh Nguyen |
| 11:30 AM – 11:45 AM |
19. Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs Mohamed Mouhajir, Limei Wang, El Houcine Bergou, Hajar El Hammouti, Lamiae Azizi and Dongqi Fu |
Lunch Break (11:45 AM - 1:00 PM)
Keynote and Panel Session (1:00 PM - 3:00 PM)
| 1:00 PM - 1:45 PM |
Keynote: AI Technologies for Target-Driven Small Molecule Drug Discovery and Development Prof. Sun Kim |
| 1:45 PM - 2:00 PM | Award Ceremony |
| 2:00 PM - 3:00 PM |
Panel Discussion: Fireside Chat: 25 Years of Biocomputing Panelists: Prof. Jake Chen, Prof. Sun Kim and Prof. Wei Wang |
Coffee Break (3:00 PM - 3:30 PM)
AI4Sciences Track Lightning Talks (3:30 PM - 4:30 PM)
| 3:30 PM - 3:40 PM |
67. Concord: Building Consensus Representations for Single Cells with Collaborative Random Projection Presenter: Xiaobo Sun |
| 3:40 PM - 3:50 PM |
753. Language-Enhanced Representation Learning for Single-Cell Transcriptomics Presenter: Zhiyuan Liu |
| 3:50 PM - 4:00 PM |
76. Enhancing Protein Representation Learning via Manifold Restore Mixing Presenter: Yizhou Dang |
| 4:00 PM - 4:10 PM |
423. Prior-Guided Multi-Omic Transformers for Single-Cell Gene Regulatory Network Inference Presenter: Tianyang Xu |
| 4:10 PM - 4:20 PM |
69. Geometry-Preserving Supervised Biological Sequence Design Presenter: Petko Bogdanov |
| 4:20 PM - 4:30 PM |
205. Caduceus: MoE Foundation Models for Unifying Biological and Natural Language Presenter: Mingze Yin |