Shannon information was defined for characterizing the uncertainty information of classical probabilistic distributions. As an uncertainty measure it is generally believed to be positive. This holds for any information quantity from two random variables because of the polymatroidal axioms. However, it is unknown why there is negative information for more than two random variables on finite dimensional spaces. We first show the negative tripartite Shannon mutual information implies specific Bayesian network representations of its joint distribution. We then show that the negative Shannon information is obtained from general tripartite Bayesian networks with quantum realizations. This provides a device-independent witness of negative Shannon information. We finally extend the result for general networks. The present result shows new insights in the network compatibility from non-Shannon information inequalities.