We also compared the performance of our method OptDis against implementations of existing subnetwork-based methods, one based on mutual information (GreedyMI) (Chuang et al., 2007), and another based on dense subnetworks (we denote as Dense) using the STRING functional network (Dao et al., 2010).
One interesting feature of GENIE3 is its potential ability to predict directed networks, while methods based on mutual information or correlation are only able to predict undirected networks.
A C3Net infers a core structure of a GRN and thus infers only a subnetwork of other GRN inference methods based on mutual information [ 10].
In contrast, methods based on mutual information capture non-linear as well as linear interactions but are applicable only to discrete data and need to employ discretization methods, which can be computationally demanding.
The sensitivity of CAPS to identify coevolution between pairs of amino acid sites that are functionally linked has been shown to outperform other methods based on mutual information content or on other models of coevolution [ 71].
Nonlinear bSPM involve mutual information (Quian Quiroga et al. 2002 ), nonlinear regression (Pijn 1990 ; Wendling et al. 2001 ), methods based on mutual phase locking and synchronization (Tass et al. 1998 ; Chavez et al. 2003 ; Stam et al. 2007 ), polyspectra methods, and a family of methods based on nonlinear dynamics (Kantz and Schreiber 2004 ; Stam 2005 ).
We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds.
Among others, sophisticated methods such as QDB and the method based on mutual information performed better than the rest as expected.
Hirschmüller proposed a semi-global method based on mutual information [11].
For the feature selection step they used a method based on Mutual Information (MI) along with some influence from the minimal Redundancy-Maximal-Relevance criterion (mRMR).
