As a principled method for partial correlation estimation, sparse inverse covariance estimation (SICE) has been employed to model brain connectivity networks, which holds great promise for brain disease diagnosis. For each subject, the SICE method naturally leads to a set of connectivity networks with various sparsity. However, existing methods usually select a single network from them for classification and the discriminative power of this set of networks has not been fully exploited. This paper argues that the connectivity networks at different sparsity levels present complementary connectivity patterns and therefore they should be jointly considered to achieve high classification performance.In this paper, we propose a subject-adaptive method to integrate multiple SICE networks as a unified representation for classification. The integration weight is learned adaptively for each subject in order to endow the method with the flexibility in dealing with subject variations. Furthermore, to respect the manifold geometry of SICE networks, Stein kernel is employed to embed the manifold structure into a kernel-induced feature space, which allows a linear integration of SICE networks to be designed. The optimization of the integration weight and the classification of the integrated networks are performed via a sparse representation framework. Through our method, we provide a unified and effective network representation that is transparent to the sparsity level of SICE networks, and can be readily utilized for further medical analysis. Experimental study on ADHD and ADNI data sets demonstrates that the proposed integration method achieves notable improvement of classification performance in comparison with methods using a single sparsity level of SICE networks and other commonly used integration methods, such as Multiple Kernel Learning.