Abstract Abductive inference is an important AI reasoning technique to fifind explanations of observations, and has recently been applied to scientifific discovery. To fifind best hypotheses among many logically possible hypotheses, we need to evaluate hypotheses obtained from the process of hypothesis generation. We propose an abductive inference architecture combined with an EM algorithm working on binary decision diagrams (BDDs). This work opens a way of applying BDDs to compress multiple hypotheses and to select most probable ones from them. An implemented system has been applied to inference of inhibition in metabolic pathways in the domain of systems biology