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bioRxiv · 10.1101/254003

Parametric and Non-parametric Gradient Matching for Network Inference

Dony, L.·He, F.·Stumpf, M.
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Abstract

Reverse engineering of gene regulatory networks from time series gene-expression data is a challenging problem, not only because of the vast sets of candidate interactions but also due to the stochastic nature of gene expression. To avoid the computational cost of large-scale simulations, a two-step Gaussian process interpolation based gradient matching approach has been proposed to solve differential equations approximately. Based on this gradient matching approach, we evaluate the fits of parametric as well as non-parametric candidate models to the data under various settings for different inference objectives. We also use model averaging, based on the Bayesian Information Criterion (BIC), in order to combine the different inferences. We found that parametric methods can provide comparable, and often improved inference compared to non-parametric methods; the latter, however, require no kinetic information and are computationally more efficient.\n\nThe code used in this work is available at https://github.com/ld2113/Final-Project.

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Dony, L., He, F., Stumpf, M.. 2018-01-25. Parametric and Non-parametric Gradient Matching for Network Inference. https://doi.org/10.1101/254003

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