Multi-layer Bundling as a New Approach for Determining Multi-scale Correlations Within a High-Dimensional Dataset

The growing complexity of biological data has spurred the development of innovative computational techniques to extract meaningful information and uncover hidden patterns within vast datasets. Biological networks, such as gene regulatory networks and protein-protein interaction networks, hold critical insights into biological features' connections and functions. Integrating and analyzing high-dimensional data, particularly in gene expression studies, stands prominent among the challenges in deciphering these networks. Clustering methods play a crucial role in addressing these challenges, with spectral clustering emerging as a potent unsupervised technique considering intrinsic geometric structures. However, spectral clustering's user-defined cluster number can lead to inconsistent and sometimes orthogonal clustering regimes. We propose the Multi-layer Bundling (MLB) method to address this limitation, combining multiple prominent clustering regimes to offer a comprehensive data view. We call the outcome clusters "bundles". This approach refines clustering outcomes, unravels hierarchical organization, and identifies bridge elements mediating communication between network components. By layering clustering results, MLB provides a global-to-local view of biological feature clusters enabling insights into intricate biological systems. Furthermore, the method enhances bundle network predictions by integrating the bundle co-cluster matrix with the affinity matrix. The versatility of MLB extends beyond biological networks, making it applicable to various domains where understanding complex relationships and patterns is needed.