OBJECTIVE To provide help for further exploring the mechanism of action of traditional Chinese herb by constructing a complex network of traditional Chinese herb-gene-protein, optimizing the mining method of potential associated genes of traditional Chinese herb and improving the mining efficiency of traditional Chinese herb system biology information.

METHODS A graph neural network model HERBGAT with an attention mechanism was proposed. A small amount of traditional Chinese herb-related gene data in the public data platform was used as input, and deep mining was performed in the traditional Chinese herb-gene-protein complex network to output potential traditional Chinese herb-related genes. The prediction results were analyzed by disease association analysis and KEGG signaling pathway analysis on the bioinformatics platform to clarify their mechanism of action, and the prediction results were verified by the literature retrieval platform.

RESULTS The training results showed that the average prediction accuracy of the HERBGAT model could reach 94%. Compared with the other two advanced complex network mining methods, HERBGAT showed better performance in the three indicators of ACC, AUC and AUPR. In the literature verification stage, the model prediction results were verified by TCM clinical literature and modern pharmacology literature, showing the good effect of HERBGAT in practical application. At the end of this paper, taking the HERBGAT model and the improved EMOGI model to explore the mechanism of action of Pinellia ternata in treating lung cancer as an example, 199 potential associated genes of Pinellia ternata in treating lung cancer were found, and these potential associated genes were preliminarily analyzed and discussed with the help of bioinformatics methods.

CONCLUSION The HERBGAT model can effectively mine potential traditional Chinese herb-associated genes, improve the mining efficiency of traditional Chinese herb-gene-protein complex networks, provide new ideas and references for the optimization of traditional Chinese herb system biology information mining methods, and provide data basis and experimental direction for exploring the mechanism of action of traditional Chinese herb.