Quantitatively identifying direct dependencies between variables is an important task in data analysis, in particular for reconstructing various types of networks and causal relations in science and engineering. One of the most widely used criteria is partial correlation, but it can only measure linearly direct association and miss nonlinear associations. However, based on conditional independence, conditional mutual information (CMI) is able to quantify nonlinearly direct relationships among variables from the observed data, superior to linear measures, but suffers from a serious problem of underestimation, in particular for those variables with tight associations in a network, which severely limits its applications. In this work, we propose a new concept, “partial independence,” with a new measure, “part mutual information” (PMI), which not only can overcome the problem of CMI but also retains the quantification properties of both mutual information (MI) and CMI. Specifically, we first defined PMI to measure nonlinearly direct dependencies between variables and then derived its relations with MI and CMI. Finally, we used a number of simulated data as benchmark examples to numerically demonstrate PMI features and further real gene expression data from Escherichia coli and yeast to reconstruct gene regulatory networks, which all validated the advantages of PMI for accurately quantifying nonlinearly direct associations in networks.

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We propose a numerical approach to solve variational problems on manifolds represented by the grid based particle method (GBPM) recently developed in Leung et al. (J. Comput. Phys. 230(7):25402561, 2011), Leung and Zhao (J. Comput. Phys. 228:77067728, 2009a, J. Comput. Phys. 228:29933024, 2009b, Commun. Comput. Phys. 8:758796, 2010). In particular, we propose a splitting algorithm for image segmentation on manifolds represented by unconnected sampling particles. To develop a fast minimization algorithm, we propose a new splitting method by generalizing the augmented Lagrangian method. To efficiently implement the resulting method, we incorporate with the local polynomial approximations of the manifold in the GBPM. The resulting method is flexible for segmentation on various manifolds including closed or open or even surfaces which are not orientable.