BACKGROUND: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. RESULTS: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. CONCLUSIONS: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses.

The symmetric kernel-driven operator equations play an important role in mathematical physics, engineering, atmospheric image processing and remote sensing sciences. Such problems are usually ill-posed in the sense that even if a unique solution exists, the solution need not depend continuously on the input data. One common technique to overcome the difficulty is applying the Tikhonov regularization to the symmetric kernel operator equations, which is more generally called the Lavrentiev regularization. It has been shown that the iterative implementation of the Tikhonov regularization can improve the rate of convergence. Therefore in this paper, we study the iterative Lavrentiev regularization method in a similar way when applying it to symmetric kernel problems which appears frequently in applications, say digital image restoration problems. We first prove the convergence property, and then under the widely used Morozov discrepancy principle(MDP), we prove the regularity of the method. Numerical performance for digital image restoration is included to confirm the theory. It seems that the iterated Lavrentiev regularization with the MDP strategy is appropriate for solving symmetric kernel problems.