LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

A combinatorial approach to biological structures and networks in predictive medicine

This work concerns the study of combinatorial models for biological structures and networks as motivated by questions in predictive medicine. Through multiple examples, the power of combinatorial models to simplify problems and facilitate computation is explored. First, continuous time Markov models are used as a model to study the progression of Alzheimer’s disease and identify which variables best predict progression at each stage. Next, RNA secondary structures are modeled by a thermodynamic Gibbs distribution on plane trees. The limiting distribution (as the number of edges in the tree goes to infinity) is studied to gain insight into the limits of the model. Additionally, a Markov chain is developed to sample from the distribution in the finite case, creating a tool for understanding what tree properties emerge from the thermodynamics. Finally, knowledge graphs are used to encode relationships extracted from the biomedical literature, and algorithms for efficient computation on these graphs are explored.Ph.D