A Construction Method for a Dynamic Weighted Protein Network Using Multi-Level Embedding

The rapid development of high-throughput technology has generated a large amount of protein–protein interaction (PPI) data, which provide a large amount of data support for constructing dynamic protein–protein interaction networks (PPINs). Constructing dynamic PPINs and applying them to recognize protein complexes has become a hot research topic. Most existing methods for complex recognition cannot fully mine the information of PPINs. To address this problem, we propose a construction method of dynamic weighted protein network by multi-level embedding (DWPNMLE). It can reflect the protein network’s dynamics and the protein network’s higher-order proximity. Firstly, the protein active period is calculated to divide the protein subnetworks at different time points. Then, the connection probability is used for the proteins possessing the same time points to judge whether there is an interaction relationship between them. Then, the corresponding protein subnetworks (multiple adjacency matrices) are constructed. Secondly, the multiple feature matrices are constructed using one-hot coding with the gene ontology (GO) information. Next, the first embedding is performed using variational graph auto-encoders (VGAEs) to aggregate features efficiently, followed by the second embedding using deep attributed network embedding (DANE) to strengthen the node representations learned in the first embedding and to maintain the first-order and higher-order proximity of the original network; finally, we compute the cosine similarity to obtain the final dynamic weighted PPIN. To evaluate the effectiveness of DWPNMLE, we apply four classical protein-complex-recognition algorithms on the DWPNMLE and compare them with two other dynamic protein network construction methods. The experimental results demonstrate that DWPNMLE significantly enhances the accuracy of complex recognition with high robustness, and the algorithms’ efficiency is also within a reasonable range.