In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses two types of heterogeneity. The first one is the type of data, such as metabolomics, proteomics and RNAseq data in genomics. These different omics data reflect the properties of the studied biological system from different perspectives. The second one is the type of scale, which indicates the measurements obtained at different scales, such as binary, ordinal, interval and ratio-scaled variables. In this thesis, we developed several statistical methods capable to fuse data sets of these two types of heterogeneity. The advantages of the proposed methods in comparison with other approaches are assessed using comprehensive simulations as well as the analysis of real biological data sets.

Multiple sets of measurements on the same objects obtained from different platforms may reflect partially complementary information of the studied system. The integrative analysis of such data sets not only provides us with the opportunity of a deeper understanding of the studied system, but also introduces some new statistical challenges. First, the separation of information that is common across all or some of the data sets, and the information that is specific to each data set is problematic. Furthermore, these data sets are often a mix of quantitative and discrete (binary or categorical) data types, while commonly used data fusion methods require all data sets to be quantitative. In this paper, we propose an exponential family simultaneous component analysis (ESCA) model to tackle the potential mixed data types problem of multiple data sets. In addition, a structured sparse pattern of the loading matrix is induced through a nearly unbiased group concave penalty to disentangle the global, local common and distinct information of the multiple data sets. A Majorization-Minimization based algorithm is derived to fit the proposed model. Analytic solutions are derived for updating all the parameters of the model in each iteration, and the algorithm will decrease the objective function in each iteration monotonically. For model selection, a missing value based cross validation procedure is implemented. The advantages of the proposed method in comparison with other approaches are assessed using comprehensive simulations as well as the analysis of real data from a chronic lymphocytic leukaemia (CLL) study.