In this paper, we propose a fuzzy neural network to enhance the learning ability of FCMs so that the automatic determination of membership functions and quantification of causalities can be incorporated with the inference mechanism of conventional FCMs.
For E. coli all available microarray experiments in the Stanford Microarray Database (SMD, see http://genome-www5.stanford.edu) were incorporated in the inference algorithm, except by experiments that increased the number of false positives (see Assessing Inference Success below); 107 experiments were selected in total from SMD.
The Bayesian methods also allow prior information to be incorporated into the inference if such information is available.
Prior knowledge may be incorporated into the inference method in order to improve accuracy and can also increase efficiency by reducing the search space.
Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models.
Wang et al. proposed to incorporate prior knowledge into the inference of conserved networks in a single condition by adjusting the Lasso penalties [ 20].
We extend the recently published Inferelator approach for GRN inference (Bonneau et al., 2006, 2007; Greenfield et al., 2010; Madar et al., 2010) to incorporate structure priors into the inference procedure.
The sampling scheme of the BNs-I is the same of the BNs and is given by Equation 2. In order to be able to incorporate extra knowledge in the inference of networks it is necessary to define a function that measures the agreement between a given network structure and the extra knowledge that we have at our disposal,.
Incorporating such random knowledge, the inference results will deviate from the purely data-driven result.
In recent years, new parametric statistical approaches have been developed in biogeography to incorporate the time dimension into the inference and as a response to what was perceived as the major weakness of the parsimony approach (Ree and Sanmartín 2009; Sanmartín 2010).
