Growing evidence shows that microbes in human body and body surface play critical roles in the development of many human diseases. Predicting the underlying associations between diseases and microbes is essential for deeply understanding the pathogenesis of diseases. However, biological experiments to find the relationship between microbes and diseases is usually laborious and time-consuming, which presents the need for effective computational tools. In this study, we propose a computational model of node-information-based Link Propagation for Human Microbe-Disease Association prediction (LPHMDA) to prioritize disease-related microbes. LPHMDA and 3 popular methods including KATZHMDA, PBHMDA, and LRLSHMDA were implemented and compared on the Human Microbe-Disease Association Database (HMDAD) based on cross-validation. As a result, LPHMDA achieved an AUC of 0.9135 in leave-one-out cross-validation (LOOCV), outperforming those of the 3 compared methods. In addition, the performances of LPHDMA on the 3-fold CV, 5-fold CV and 10-fold CV were also better than those of the other 3 canonical methods, further demonstrating its superiority. Finally, we took colorectal carcinoma, asthma and obesity as case studies. Interestingly, 9, 9 and 8 of the top 10 novel microbes predicted by LPHMDA to be associated with the 3 diseases respectively could be confirmed by literatures, providing potential disease-associated microbes for further experimental validation. In summary, LPHMDA is an effective method for prioritizing disease-associated microbes.

中文翻译：

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利用基于节点信息的链路传播方法优先考虑人类微生物-疾病关联


越来越多的证据表明，人体和体表微生物在许多人类疾病的发生发展中发挥着关键作用。预测疾病和微生物之间的潜在关联对于深入了解疾病的发病机制至关重要。然而，寻找微生物与疾病之间关系的生物实验通常既费力又费时，这就需要有效的计算工具。在这项研究中，我们提出了一种基于节点信息的人类微生物-疾病关联预测链接传播（LPHMDA）的计算模型，以优先考虑与疾病相关的微生物。基于交叉验证，在人类微生物疾病协会数据库（HMDAD）上实施并比较了 LPHMDA 和 3 种流行方法（包括 KATZHMDA、PBHMDA 和 LRLSHMDA）。结果，LPHMDA 在留一交叉验证 (LOOCV) 中的 AUC 为 0.9135，优于 3 种比较方法。此外，LPHDMA在3倍CV、5倍CV和10倍CV上的性能也优于其他3种经典方法，进一步证明了其优越性。最后，我们以结直肠癌、哮喘和肥胖作为案例研究。有趣的是，LPHMDA预测与3种疾病相关的前10位新型微生物中，分别有9、9和8种得到文献证实，为进一步的实验验证提供了潜在的疾病相关微生物。总之，LPHMDA 是一种优先考虑疾病相关微生物的有效方法。