5 papers
ExPath: Targeted Pathway Inference for Biological Knowledge Bases via Graph Learning and Explanation
Rikuto Kotoge, Ziwei Yang, Zheng Chen +4
Retrieving targeted pathways in biological knowledge bases, particularly when incorporating wet-lab experimental data, remains a challenging task and often requires downstream anal…
DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research
Zifeng Wang, Zheng Chen, Ziwei Yang +5
Biomedical knowledge graphs (KGs) encode vast, heterogeneous information spanning literature, genes, pathways, drugs, diseases, and clinical trials, but leveraging them collectivel…
MLOmics: Cancer Multi-Omics Database for Machine Learning
Ziwei Yang, Rikuto Kotoge, Xihao Piao +6
Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these su…
Can Large Language Models Replace Data Scientists in Biomedical Research?
Zifeng Wang, Benjamin Danek, Ziwei Yang +2
Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown…
GeSubNet: Gene Interaction Inference for Disease Subtype Network Generation
Ziwei Yang, Zheng Chen, Xin Liu +5
Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, i…