Various microbes have proved to be closely related to the pathogenesis of human diseases. While many computational methods for predicting human microbe-disease associations (MDAs) have been developed, few systematic reviews on these methods have been reported. In this study, we provide a comprehensive overview of the existing methods. Firstly, we introduce the data used in existing MDA prediction methods. Secondly, we classify those methods into different categories by their nature and describe their algorithms and strategies in detail. Next, experimental evaluations are conducted on representative methods using different similarity data and calculation methods to compare their prediction performances. Based on the principles of computational methods and experimental results, we discuss the advantages and disadvantages of those methods and propose suggestions for the improvement of prediction performances. Considering the problems of the MDA prediction at present stage, we discuss future work from three perspectives including data, methods and formulations at the end.

中文翻译：

---

预测微生物-疾病关联的调查：生物数据和计算方法

各种微生物已被证明与人类疾病的发病机制密切相关。虽然已经开发了许多用于预测人类微生物疾病关联 (MDA) 的计算方法，但很少有关于这些方法的系统评价的报道。在本研究中，我们对现有方法进行了全面概述。首先，我们介绍现有MDA预测方法中使用的数据。其次，我们根据它们的性质将这些方法分为不同的类别，并详细描述它们的算法和策略。接下来，使用不同的相似性数据和计算方法对代表性方法进行实验评估，以比较它们的预测性能。根据计算方法原理和实验结果，我们讨论了这些方法的优缺点，并提出了提高预测性能的建议。针对现阶段MDA预测存在的问题，最后从数据、方法和公式三个角度讨论了未来的工作。