HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Online Publication Date2017-08-07
Print Publication Date2017-12-15
Permanent link to this recordhttp://hdl.handle.net/10754/626582
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AbstractMotivation: The use of differential equations (ODE) is one of the most promising approaches to network inference. The success of ODE-based approaches has, however, been limited, due to the difficulty in estimating parameters and by their lack of scalability. Here, we introduce a novel method and pipeline to reverse engineer gene regulatory networks from gene expression of time series and perturbation data based upon an improvement on the calculation scheme of the derivatives and a pre-filtration step to reduce the number of possible links. The method introduces a linear differential equation model with adaptive numerical differentiation that is scalable to extremely large regulatory networks. Results: We demonstrate the ability of this method to outperform current state-of-the-art methods applied to experimental and synthetic data using test data from the DREAM4 and DREAM5 challenges. Our method displays greater accuracy and scalability. We benchmark the performance of the pipeline with respect to dataset size and levels of noise. We show that the computation time is linear over various network sizes.
CitationDeng Y, Zenil H, Tegnér J, Kiani NA (2017) HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation. Bioinformatics 33: 3964–3972. Available: http://dx.doi.org/10.1093/bioinformatics/btx501.
SponsorsVinnova VINNMER fellowship, Stratneuro (to N.A.K.); Swedish Research Council - Vetenskapsra°det (to H.Z.). The founders played no role in the design of the study, in data collection and analysis, in the decision to publish, or in the preparation of the manuscript.
PublisherOxford University Press (OUP)