Constraint programming in community-based gene regulatory network inference

Gene Regulatory Network (GRN) inference is a major objective of Systems Biology. The complexity of biological systems and the lack of adequate data have posed many challenges to the inference problem. Community networks integrate predictions from individual methods in a "meta predictor", in order to compose the advantages of different methods and soften individual limitations. This paper proposes a novel methodology to integrate prediction ensembles using Constraint Programming, a declarative modeling paradigm, which allows the formulation of dependencies among components of the problem, enabling the integration of diverse forms of knowledge. The paper experimentally shows the potential of this method: the addition of biological constraints can offer improvements in the prediction accuracy, and the method shows promising results in assessing biological hypothesis using constraints.