A Binary Classifier for Prediction of the Types of Metabolic Pathway of Chemicals
A Binary Classifier for Prediction of the Types of Metabolic Pathway of Chemicals
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DOI：
10.2174/1386207319666161215142130
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发表时间：
2017-01-01
影响因子：
1.8
通讯作者：
Chen, Lei
中科院分区：
文献类型：
--
作者：
Fang, Yemin;Chen, Lei
背景：代谢途径的研究是生物化学的重要领域之一。对代谢途径系统的深入理解有助于揭示某些基本生物学过程的机制。由于化学物质是代谢途径的主要组成部分，因此正确识别给定化学物质可以参与哪些代谢途径是理解代谢途径系统的重要步骤。以往的方法大多只考虑化学物质的信息，试图解决将化学物质分配到合适的代谢途径的多标记分类问题。方法：在本研究中，也使用了途径信息，从而将问题转化为识别化学物质和代谢途径对的二进制分类问题，即，将化学和代谢途径配对作为本研究中要考虑的样品。为了构建预测模型，通过整合化学品之间的关联和途径类型之间的关联来评估化学途径类型对之间的关联。结果：大量的测试表明，所构建的模型具有良好的预测性能，总的预测精度在0.878左右。结论：比较结果表明，该模型是相当有效的，适用于识别特定的化学物质是否可以参与特定的代谢途径。
Background: The study of metabolic pathway is one of the most important fields in biochemistry. Good comprehension of the metabolic pathway system is helpful to uncover the mechanism of some fundamental biological processes. Because chemicals are part of the main components of the metabolic pathway, correct identification of which metabolic pathways a given chemical can participate in is an important step for understanding the metabolic pathway system. Most previous methods only considered the chemical information, which tried to deal with a multilabel classification problem of assigning chemicals to proper metabolic pathways.Methods: In this study, the pathway information was also employed, thereby transforming the problem into a binary classification problem of identifying the pair of chemicals and metabolic pathways, i.e., a chemical and a metabolic pathway was paired as a sample to be considered in this study. To construct the prediction model, the association between chemical pathway type pairs was evaluated by integrating the association between chemicals and association between pathway types. The support vector machine was adopted as the prediction engine.Results: The extensive tests show that the constructed model yields good performance with total prediction accuracy around 0.878.Conclusion: The comparison results indicate that our model is quite effective and suitable for the identification of whether a given chemical can participate in a given metabolic pathway.