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  "Description": "Simultaneously clusters the Periodontal diseases (PD)\npatients and their tooth sites after taking the patient- and\nsite-level covariates into consideration. 'BAREB' uses the\ndeterminantal point process (DPP) prior to induce diversity\namong different biclusters to facilitate parsimony and\ninterpretability. Essentially, 'BAREB' is a cluster-wise linear\nmodel based on Yuliang (2020) <doi:10.1002/sim.8536>.",
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