预答辩公告

学位论文简介

人体微生物与人类健康息息相关，其菌落生态失衡可能导致复杂的人体疾病，因此微生物被认为是最新的治疗靶标。目前关于人体微生物网络的关系识别研究是生物信息学研究领域的研究热点之一。因此，文本围绕人体微生物，探索微生物在复杂疾病中的作用机制以及其在药物治疗过程中的功能机制，提出了多种可用于系统识别致病微生物以及其与药物相互作用关系的计算模型。取得了以下主要创新性研究成果：

1. 提出了一种基于改进随机游走的半监督算法NTSHMDA预测微生物-疾病关联关系。通过融合网络拓扑相似性对传统随机游走算法进行了改进，改善了已有算法预测表现。

2. 提出了一种基于图注意力网络和矩阵填充的深度学习模型GATMDA预测微生物-疾病关联关系。本文首次将图注意力网络应用于该研究领域，解决了新微生物和新疾病相关预测问题。

3. 提出了一种基于图卷积神经网络的微生物-药物预测模型GCNMDA，为候选化合物的选择提供了有力筛选工具。该模型有效结合了图卷积网络、条件随机场以及注意力机制等多种技术设计了高效的表征学习模块。

4. 提出了一种基于集成图注意力网络的微生物-药物预测模型EGATMDA。该模型为图注意力网络在该研究领域的首次应用，实现了对于新微生物和新药物的相关预测。

主要学术成果

1. Yahui Long, Jiawei Luo, Yu Zhang and Yan Xia. Predicting Human Microbe-Disease Associations via Graph Attention Networks with Inductive Matrix Completion. Briefings in Bioinformatics. 2020. (SCI 1区)

2. Yahui Long, Min Wu, Yong Liu, Jie Zheng, Chee-Keong Kwoh, Jiawei Luo and Xiaoli Li. Graph Contextualized Attention Network for Predicting Synthetic Lethality in Human Cancers. Bioinformatics. 2021. (SCI 2区)

3. Yahui Long, Min Wu, Chee-Keong Kwoh, Jiawei Luo and Xiaoli Li. Predicting Human Microbe-Drug Associations via Graph Convolutional Network with Conditional Random Field. Bioinformatics. 36(19), 4918-4927, 2020. (SCI 2区)

4. Yahui Long, Min Wu, Yong Liu, Chee-Keong, Kwoh, Jiawei Luo and Xiaoli Li. Ensembling graph attention networks for human microbe-drug association prediction. Bioinformatics. 36, i779-i786, 2020. (SCI 2区)

5. Yahui Long and Jiawei Luo. Association mining to identify microbe drug interactions based on heterogeneous network embedding representation. IEEE Journal of Biomedical and Health Informatics (J-BHI). 25(01), 266-275, 2020. (SCI 2区)

6. Yahui Long, Yu Zhang, Min Wu, Shaoliang Peng, Chee-Keong Kwoh, Jiawei Luo and Xiaoli Li. Predicting Drugs for COVID-19/SARS-CoV-2 via Heterogeneous Graph Attention Networks. Methods. 2021. (SCI 2区, 被推荐发表)

7. Jiawei Luo and Yahui Long. NTSHMDA: Prediction of human microbe-disease association based on random walk by integrating network topological similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 17(4), 1341-1351, 2018. (CCF B类推荐期刊，导师一作)

8. Yahui Long and Jiawei Luo. WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network. BMC Bioinformatics. 20:541, 2019. (SCI 3区)

9. Yu Zhang, Yahui Long, Rui Yin, Chee-Keong Kwoh. DL-CRISPR: A Deep Learning Method for Off-Target Activity Prediction in CRISPR/Cas9 With Data. IEEE Access, 2020. (SCI 2区)

10. Yu Zhang, Yahui Long, Chee-Keong, Kwoh. Deep learning based DNA: RNA triplex forming potential prediction. BMC Bioinformatics, 2020. (SCI 3区)