YZS-model: A Predictive Model for Organic Drug Solubility Based on Graph Convolutional Networks and Transformer-Attention

• URL: http://arxiv.org/abs/2406.19136v6
• Date: Tue, 13 Aug 2024 07:12:37 GMT
• Title: YZS-model: A Predictive Model for Organic Drug Solubility Based on Graph Convolutional Networks and Transformer-Attention
• Authors: Chenxu Wang, Haowei Ming, Jian He, Yao Lu, Junhong Chen,
• Abstract summary: Traditional methods often miss complex molecular structures, leading to inaccuracies. We introduce the YZS-Model, a deep learning framework integrating Graph Convolutional Networks (GCN), Transformer architectures, and Long Short-Term Memory (LSTM) networks. YZS-Model achieved an $R2$ of 0.59 and an RMSE of 0.57, outperforming benchmark models.
• Score: 9.018408514318631
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Accurate prediction of drug molecule solubility is crucial for therapeutic effectiveness and safety. Traditional methods often miss complex molecular structures, leading to inaccuracies. We introduce the YZS-Model, a deep learning framework integrating Graph Convolutional Networks (GCN), Transformer architectures, and Long Short-Term Memory (LSTM) networks to enhance prediction precision. GCNs excel at capturing intricate molecular topologies by modeling the relationships between atoms and bonds. Transformers, with their self-attention mechanisms, effectively identify long-range dependencies within molecules, capturing global interactions. LSTMs process sequential data, preserving long-term dependencies and integrating temporal information within molecular sequences. This multifaceted approach leverages the strengths of each component, resulting in a model that comprehensively understands and predicts molecular properties. Trained on 9,943 compounds and tested on an anticancer dataset, the YZS-Model achieved an $R^2$ of 0.59 and an RMSE of 0.57, outperforming benchmark models ($R^2$ of 0.52 and RMSE of 0.61). In an independent test, it demonstrated an RMSE of 1.05, improving accuracy by 45.9%. The integration of these deep learning techniques allows the YZS-Model to learn valuable features from complex data without predefined parameters, handle large datasets efficiently, and adapt to various molecular types. This comprehensive capability significantly improves predictive accuracy and model generalizability. Its precision in solubility predictions can expedite drug development by optimizing candidate selection, reducing costs, and enhancing efficiency. Our research underscores deep learning's transformative potential in pharmaceutical science, particularly for solubility prediction and drug design.

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