Natasa Miskov-Zivanov Research Group

University of Pittsburgh-Pittsburgh campus

How can automated knowledge extraction produce executable mechanistic models that explain cellular behavior? The MeLoDy Lab develops computational methods and an explainable-AI tool ecosystem (BOHEME) to convert literature-derived knowledge into executable biological models. The group builds modular workflows that extract biological interactions, verify evidence across databases, reconcile heterogeneous graphs, and assemble mechanistic models for simulation and hypothesis generation. Projects include ACCORDION, CLARINET, FLUTE, and BioRECIPE for context-aware knowledge selection, reliable model recommendation, and knowledge representation. Research combines knowledge engineering, graph algorithms, mechanistic modeling, and machine learning to scale model building alongside expanding biomedical literature.