MIFNN: Molecular Information Feature Extraction and Fusion Deep Neural Network for Screening Potential Drugs

• Published in: Current Issues in Molecular Biology Vol. 44; no. 11; pp. 5638 - 5654
• Main Authors: Wang, Jingjing, Li, Hongzhen, Zhao, Wenhan, Pang, Tinglin, Sun, Zengzhao, Zhang, Bo, Xu, Huaqiang
• Format: Journal Article
• Language: English
• Published: MDPI AG 13.11.2022; MDPI
• Subjects: Algorithms; Analysis; attention mechanism; Computational linguistics; deep learning; Drug discovery; feature fusion; Language processing; Mathematical optimization; Natural language interfaces; Neural networks; particle swarm optimization; support vector machine; Taiwan
• ISSN: 1467-3045; 1467-3037; 1467-3045
• DOI: 10.3390/cimb44110382

Molecular property prediction is essential for drug screening and reducing the cost of drug discovery. Current approaches combined with deep learning for drug prediction have proven their viability. Based on the previous deep learning networks, we propose the Molecular Information Fusion Neural Network (MIFNN). The features of MIFNN are as follows: (1) we extracted directed molecular information using 1D-CNN and the Morgan fingerprint using 2D-CNN to obtain more comprehensive feature information; (2) we fused two molecular features from one-dimensional and two-dimensional space, and we used the directed message-passing method to reduce the repeated collection of information and improve efficiency; (3) we used a bidirectional long short-term memory and attention module to adjust the molecular feature information and improve classification accuracy; (4) we used the particle swarm optimization algorithm to improve the traditional support vector machine. We tested the performance of the model on eight publicly available datasets. In addition to comparing the overall classification capability with the baseline model, we conducted a series of ablation experiments to verify the optimization of different modules in the model. Compared with the baseline model, our model achieved a maximum improvement of 14% on the ToxCast dataset. The performance was very stable on most datasets. On the basis of the current experimental results, MIFNN performed better than previous models on the datasets applied in this paper.