A challenge in computational biology is to uncover the gene-protein inter-actions from gene expression data. A good approach for discovering inter-actions between genes based on multiple expression measurements is to use Bayesian networks. To that end, BUBBLE (Bayesian User Based Bio-logical Learning Environment) has been developed. BUBBLE allows a re-searcher to create pathways, to specify prior constraints, to import data from various databases and learn a Bayesian network model. In addition, User Relevance Feedback queries the user with optimal chosen questions to improve the correctness...