Parameter identifiability-based optimal observation remedy for biological networks

BACKGROUND: To systematically understand the interactions between numerous biological components, a variety of biological networks on different levels and scales have been constructed and made available in public databases or knowledge repositories. Graphical models such as structural equation models have long been used to describe biological networks for various quantitative analysis tasks, especially key biological parameter estimation. However, limited by resources or technical capacities, partial observation is a common problem in experimental observations of biological networks, and it thus becomes an important problem how to select unobserved nodes for additional measurements such that all unknown model parameters become identifiable. To the best knowledge of our authors, a solution to this problem does not exist until this study. RESULTS: The identifiability-based observation problem for biological networks is mathematically formulated for the first time based on linear recursive structural equation models, and then a dynamic programming strategy is developed to obtain the optimal observation strategies. The efficiency of the dynamic programming algorithm is achieved by avoiding both symbolic computation and matrix operations as used in other studies. We also provided necessary theoretical justifications to the proposed method. Finally, we verified the algorithm using synthetic network structures and illustrated the application of the proposed method in practice using a real biological network related to influenza A virus infection. CONCLUSIONS: The proposed approach is the first solution to the structural identifiability-based optimal observation remedy problem. It is applicable to an arbitrary directed acyclic biological network (recursive SEMs) without bidirectional edges, and it is a computerizable method. Observation remedy is an important issue in experiment design for biological networks, and we believe that this study provides a solid basis for dealing with more challenging design issues (e.g., feedback loops, dynamic or nonlinear networks) in the future. We implemented our method in R, which is freely accessible at https://github.com/Hongyu-Miao/SIOOR. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12918-017-0432-2) contains supplementary material, which is available to authorized users.