microRNA-disease关联（图中的关联、graph中的关联）预测方法分类综述（类别、分区、年份、期刊、基本内容）

英文期刊推荐和分区（2022.12最新版中科院分区）

1. 一区

2. 二区
   BMC GENOMICS
   NUCLEIC ACIDS RESEARCH 二区Top
   Iscience
   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES MDPI。二区Top, 但是水刊，一年发文万余篇
   IEEE journal of biomedical and health informatics
   PLoS Computational Biology

3. 三区
   BMC BIOINFORMATICS
   Biomolecules 生物分子
   Bioinformatics https://www.ablesci.com/journal/detail?id=MNE3pg
   COMPUTERS IN BIOLOGY AND MEDICINE
   Cells MDPI出版社2021低预警，OA
   Frontiers in Bioengineering and Biotechnology
   Frontiers in Genetics
   GENOMICS 基因学
   IEEE/ACM transactions on computational biology and bioinformatics
   Ieee Access 2020年预警过
   Methods
   RNA Biology

4. 四区
   Bmc Bioinformatics
   COMPUTATIONAL BIOLOGY AND CHEMISTRY

中文期刊推荐

T0:电子学报、通信学报
T2：Application Research of Computers 计算机应用研究

平台搭建文章

3. 三区：
   [1] ZHANG Z-W, GAO Z, ZHENG C-H, et al. WVMDA: Predicting miRNA-Disease Association Based on Weighted Voting [J]. Frontiers in genetics, 2021, 12: 742992-.
   [1] HU J, LEPORE R, DOBSON R J B, et al. DGLinker: flexible knowledge-graph prediction of disease-gene associations [J]. Nucleic acids research, 2021, 49(W1): W153-W61.

综述文章

2. 二区
   [1] MAHJOUBIN-TEHRAN M, REZAEI S, JALILI A, et al. A comprehensive review of online resources for microRNA-diseases associations: the state of the art [J]. Briefings in Bioinformatics, 2022, 23(1). 在线资源综述
   [1] YU L, ZHENG Y, JU B, et al. Research progress of miRNA-disease association prediction and comparison of related algorithms [J]. Briefings in bioinformatics, 2022.
   [1] CHEN X, XIE D, ZHAO Q, et al. MicroRNAs and complex diseases: from experimental results to computational models [J]. Brief Bioinform, 2019 综述, 20(2): 515-39.

   [1] LEI X, MUDIYANSELAGE T B, ZHANG Y, et al. A comprehensive survey on computational methods of non-coding RNA and disease association prediction [J]. Briefings in bioinformatics, 2021, 22(4). 非编码RNA综述

分类方法

我的分类方法：

1. 机器学习
   包括传统的统计机器学习、深度学习、图表示学习（图表示学习-图嵌入技术、图表示学习-图神经网络技术）

2. 矩阵变换

3. 启发式得分

不同的作者对于分类方法持有不同的观点。
下面标题的分类方法得益于2022年的综述，和关联预测的一片论文。

1Heuristic score-based method (基于启发式得分的方法）

1. 一区

2. 二区
   [1] LUO J, LIU Y, LIU P, et al. Data Integration Using Tensor Decomposition for The Prediction of miRNA-Disease Associations [J]. IEEE journal of biomedical and health informatics, 2021, PP.

3. 三区
   [1] LI X, AI H, LI B, et al. MIMRDA: A Method Incorporating the miRNA and mRNA Expression Profiles for Predicting miRNA-Disease Associations to Identify Key miRNAs (microRNAs) [J]. Front Genet, 2022, 13: 825318.
   [1] ZHOU F, YIN M-M, ZHAO J-X, et al. A Method Based on Dual-network Information Fusion to Predict MiRNA-Disease Associations [J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, PP.
   [1] ZHANG Z-W, GAO Z, ZHENG C-H, et al. WVMDA: Predicting miRNA-Disease Association Based on Weighted Voting [J]. Frontiers in genetics, 2021, 12: 742992-.
   [1] ZHANG W, LI Z, GUO W, et al. A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations [J]. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 2021, 18(2): 405-15.
   [1] YIN M-M, CUI Z, GAO M-M, et al. LWPCMF: Logistic Weighted Profile-Based Collaborative Matrix Factorization for Predicting MiRNA-Disease Associations [J]. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 2021, 18(3): 1122-9.
   [1] NIE R, LI Z, YOU Z-H, et al. Efficient framework for predicting MiRNA-disease associations based on improved hybrid collaborative filtering [J]. BMC medical informatics and decision making, 2021, 21(Suppl 1): 254-.

4. 四区

2 Embedding-based method （基于嵌入的方法）

Those methods learn node embeddings based on connections between nodes and compute similarity scores using the embeddings.
基于嵌入的方法根据节点间的链接学习节点的嵌入，然后使用嵌入计算相似度得分。（常用的计算方法有点积、拼接或者相加后使用MLP）。
基于嵌入的方法又可分很多类（基于矩阵分解、基于随机游走、基于GNN图神经网络、基于传统机器学习算法的、基于深度学习算法的）

2.1 Matrix factorization （matrix decomposition、矩阵分解）

有矩阵分解补全，归纳矩阵补全等

1. 一区

2. 二区
   [1] ZHENG X, ZHANG C, WAN C. MiRNA-Disease association prediction via non-negative matrix factorization based matrix completion [J]. Signal Processing, 2022, 190.
   [1] LI L, GAO Z, WANG Y-T, et al. SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization [J]. Plos Computational Biology, 2021, 17(7).
   [1] HUANG Z, HAN Y, LIU L, et al. LE-MDCAP: A Computational Model to Prioritize Causal miRNA-Disease Associations [J]. Int J Mol Sci, 2021, 22(24). 水刊，一年发文万余篇
   [1] HUANG F, YUE X, XIONG Z K, et al. Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations [J]. Briefings in Bioinformatics, 2021, 22(3).
   [1] DING Y, LEI X, LIAO B, et al. Predicting miRNA-Disease Associations Based on Multi-View Variational Graph Auto-Encoder with Matrix Factorization [J]. IEEE journal of biomedical and health informatics, 2021, PP.
   [1] CHEN X, SUN L G, ZHAO Y. NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion [J]. Brief Bioinform, 2021, 22(1): 485-96.

3. 三区
   [1] ZHANG S, LI J, ZHOU W, et al. Higher-Order Proximity-Based MiRNA-Disease Associations Prediction [J]. IEEE/ACM Trans Comput Biol Bioinform, 2022, 19(1): 501-12.
   [1] WANG L, ZHONG C. Prediction of miRNA-Disease Association Using Deep Collaborative Filtering [J]. Biomed Research International, 2021, 2021.
   [1] TOPRAK A, DOGAN E E. Prediction of Potential MicroRNA-Disease Association Using Kernelized Bayesian Matrix Factorization [J]. Interdisciplinary Sciences-Computational Life Sciences, 2021, 13(4): 595-602.
   [1] LU X, LI J, ZHU Z, et al. Predicting miRNA-disease associations via combining probability matrix feature decomposition with neighbor learning [J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, PP.
   [1] CHEN X, LI S X, YIN J, et al. Potential miRNA-disease association prediction based on kernelized Bayesian matrix factorization [J]. Genomics, 2020 WFY, 112(1): 809-19.

4. 四区
   [1] ZHOU F, YIN M M, JIAO C N, et al. Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations [J]. BMC Bioinformatics, 2021, 22(1): 573.
   [1] LU X, GAO Y, ZHU Z, et al. A Constrained Probabilistic Matrix Decomposition Method for Predicting miRNA-disease Associations [J]. Current Bioinformatics, 2021, 16(4): 524-33.
   [1] LU X, GAO Y, ZHU Z, et al. A Constrained Probabilistic Matrix Decomposition Method for Predicting miRNA-disease Associations [J]. Current Bioinformatics, 2021, 16(4): 524-33.
   [1] GAO Z, WANG Y T, WU Q W, et al. Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction [J]. BMC Bioinformatics, 2020, 21(1): 61.

2.2 Random walk-based embedding methods （基于随机游走嵌入的方法）

1. 一区

2. 二区
   [1] YU L, ZHENG Y, GAO L. MiRNA-disease association prediction based on meta-paths [J]. Brief Bioinform, 2022.
   [1] LI H-Y, CHEN H-Y, WANG L, et al. A structural deep network embedding model for predicting associations between miRNA and disease based on molecular association network [J]. Scientific Reports, 2021, 11(1).

3. 三区
   [1] VAN TINH N, THI TU KIEN L, KHOAT T, et al. Predicting miRNA-disease associations using improved random walk with restart and integrating multiple similarities [J]. Scientific Reports, 2021, 11(1).
   [1] QU J, WANG C-C, CAI S-B, et al. Biased Random Walk With Restart on Multilayer Heterogeneous Networks for MiRNA-Disease Association Prediction [J]. Frontiers in Genetics, 2021, 12.
   [1] LI A, DENG Y, TAN Y, et al. A novel miRNA-disease association prediction model using dual random walk with restart and space projection federated method [J]. Plos One, 2021, 16(6).

4. 四区
   [1] ZHU Q, FAN Y, PAN X. Fusing Multiple Biological Networks to Effectively Predict miRNA-disease Associations [J]. Current Bioinformatics, 2021, 16(3): 371-84.
   [1] WANG X, WANG F Y, WANG X Z, et al. DEMLP: DeepWalk Embedding in MLP for miRNA-Disease Association Prediction [J]. Journal of Sensors, 2021, 2021.

2.3 GNNs(图神经网络）

1. 一区
   [1] LI Z, ZHONG T, HUANG D, et al. Hierarchical graph attention network for miRNA-disease association prediction [J]. Mol Ther, 2022.

2. 二区
   [1] ZHONG T, LI Z, YOU Z H, et al. Predicting miRNA-disease associations based on graph random propagation network and attention network [J]. Brief Bioinform, 2022.
   [1] JIN C, SHI Z, LIN K, et al. Predicting miRNA-Disease Association Based on Neural Inductive Matrix Completion with Graph Autoencoders and Self-Attention Mechanism [J]. Biomolecules, 2022, 12(1).
   [1] ZHANG G, LI M, DENG H, et al. SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations [J]. Briefings in bioinformatics, 2021.
   [1] TANG X, LUO J, SHEN C, et al. Multi-view Multichannel Attention Graph Convolutional Network for miRNA-disease association prediction [J]. Briefings in bioinformatics, 2021.
   [1] LI Z, JIANG K, QIN S, et al. GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction [J]. Plos Computational Biology, 2021, 17(6).
   [1] LI L, WANG Y-T, JI C-M, et al. GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder [J]. PLoS computational biology, 2021, 17(12): e1009655-e.

3. 三区
   [1] YAN C, DUAN G, LI N, et al. PDMDA: Predicting deep-level miRNA-disease associations with graph neural networks and sequence features [J]. Bioinformatics, 2022.
   [1] HAN H, ZHU R, LIU J-X, et al. Predicting miRNA-disease associations via layer attention graph convolutional network model [J]. BMC medical informatics and decision making, 2022, 22(1): 69-.
   [1] YU D-L, YU Z-G, HAN G-S, et al. Heterogeneous Types of miRNA-Disease Associations Stratified by Multi-Layer Network Embedding and Prediction [J]. Biomedicines, 2021, 9(9).
   [1] WANG Y-T, WU Q-W, GAO Z, et al. MiRNA-disease association prediction via hypergraph learning based on high-dimensionality features [J]. Bmc Medical Informatics and Decision Making, 2021, 21(SUPPL 1).
   [1] PENG W, DU J L, DAI W, et al. Predicting miRNA-Disease Association Based on Modularity Preserving Heterogeneous Network Embedding [J]. Frontiers in Cell and Developmental Biology, 2021, 9.
   [1] PANG S, ZHUANG Y, WANG X, et al. EOESGC: predicting miRNA-disease associations based on embedding of embedding and simplified graph convolutional network [J]. BMC medical informatics and decision making, 2021, 21(1): 319-.
   [1] JI C, WANG Y, NI J, et al. Predicting miRNA-Disease Associations Based on Heterogeneous Graph Attention Networks [J]. Front Genet, 2021, 12: 727744.

4. 四区

2.4 基于嵌入的关联预测-统计机器学习

1. 一区

2. 二区

3. 三区
   [1] LI L, GAO Z, ZHENG C-H, et al. Predicting miRNA-Disease Association Based on Improved Graph Regression [J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, PP.

4. 四区
   [1] WU Y, ZHU D, WANG X, et al. An ensemble learning framework for potential miRNA-disease association prediction with positive-unlabeled data [J]. Comput Biol Chem, 2021, 95: 107566.

2.5 基于嵌入的关联预测-深度学习 （从多层神经网络上理解，隐藏层要超过两层）

2. 二区
   [1] WANG J, LI J, YUE K, et al. NMCMDA: neural multicategory MiRNA-disease association prediction [J]. Briefings in bioinformatics, 2021, 22(5).
   [1] LI J, LIU T, WANG J R, et al. MvKFN-MDA: Multi-view Kernel Fusion Network for miRNA-disease association prediction [J]. Artificial Intelligence in Medicine, 2021, 118: 11.
   [1] JI B-Y, YOU Z-H, WANG Y, et al. DANE-MDA: Predicting microRNA-disease associations via deep attributed network embedding [J]. Iscience, 2021, 24(6).

3. 三区
   [1] TANG M, LIU C, LIU D, et al. PMDFI: Predicting miRNA-Disease Associations Based on High-Order Feature Interaction [J]. Frontiers in Genetics, 2021, 12.
   [1] JI C, WANG Y T, GAO Z, et al. A Semi-Supervised Learning Method for MiRNA-Disease Association Prediction Based on Variational Autoencoder [J]. IEEE/ACM Trans Comput Biol Bioinform, 2021, PP.
   [1] JI C, GAO Z, MA X, et al. AEMDA: inferring miRNA-disease associations based on deep autoencoder [J]. Bioinformatics, 2021, 37(1): 66-72.

4. 四区
   [1] LIU B, ZHU X, ZHANG L, et al. Combined embedding model for MiRNA-disease association prediction [J]. Bmc Bioinformatics, 2021, 22(1).

3.Statistical machine learning-based method （统计机器学习方法）

1. 一区

2. 二区
   [1] UTHAYOPAS K, DE SA A G C, ALAVI A, et al. TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction [J]. Molecular therapy Nucleic acids, 2021, 26: 536-46. （得分太高了，但是数据不一样，可以引用）

3. 三区
   [1] ZHENG K, YOU Z-H, WANG L, et al. MISSIM: An Incremental Learning-Based Model With Applications to the Prediction of miRNA-Disease Association [J]. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 2021, 18(5): 1733-42.
   [1] YU S, WANG H. RSCMDA: Prediction of Potential miRNA-Disease Associations Based on a Robust Similarity Constraint Learning Method [J]. Interdisciplinary Sciences-Computational Life Sciences, 2021.
   [1] WANG Y-T, LI L, JI C-M, et al. ILPMDA: Predicting miRNA-Disease Association Based on Improved Label Propagation [J]. Frontiers in genetics, 2021, 12: 743665-.
   [1] DAI Q, CHU Y, LI Z, et al. MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information [J]. Computers in Biology and Medicine, 2021, 136.
   [1] CUI L, LU Y, SUN J, et al. RFLMDA: A Novel Reinforcement Learning-Based Computational Model for Human MicroRNA-Disease Association Prediction [J]. Biomolecules, 2021, 11(12).

4. 四区
   [1] TOPRAK A, ERYILMAZ E. Prediction of miRNA-disease associations based on Weighted K-Nearest known neighbors and network consistency projection [J]. Journal of Bioinformatics and Computational Biology, 2021, 19(1).
   [1] CHEN X J, HUA X Y, JIANG Z R. ANMDA: anti-noise based computational model for predicting potential miRNA-disease associations [J]. Bmc Bioinformatics, 2021, 22(1).

4.Deep learning-based method (基于深度学习的方法）

1. 1区
   1] ZHOU F, YIN M-M, JIAO C-N, et al. Predicting miRNA-Disease Associations Through Deep Autoencoder With Multiple Kernel Learning [J]. IEEE transactions on neural networks and learning systems, 2021, PP.

2. 二区
   [1] DING Y, LEI X, LIAO B, et al. MLRDFM: a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations [J]. Briefings in bioinformatics, 2022.
   [1] WANG C-C, LI T-H, HUANG L, et al. Prediction of potential miRNA-disease associations based on stacked autoencoder [J]. Briefings in bioinformatics, 2022.
   [1] XUAN P, WANG D, CUI H, et al. Integration of pairwise neighbor topologies and miRNA family and cluster attributes for miRNA-disease association prediction [J]. Briefings in bioinformatics, 2021. 一个生成性和对抗性的模型，用基于卷积自动编码器的生成器来编码miRNA-疾病对的低维拓扑结构表示
   [1] CHEN X, LI T H, ZHAO Y, et al. Deep-belief network for predicting potential miRNA-disease associations [J]. Briefings in Bioinformatics, 2021, 22(3).

3. 三区
   [1] ZHENG K, YOU Z-H, WANG L, et al. MISSIM: An Incremental Learning-Based Model With Applications to the Prediction of miRNA-Disease Association [J]. Ieee-Acm Transactions on Computational Biology and Bioinformatics, 2021, 18(5): 1733-42.
   [1] HAN G, KUANG Z, DENG L. MSCNE:Predict miRNA-Disease Associations Using Neural Network based on Multi-source Biological Information [J]. IEEE/ACM transactions on computational biology and bioinformatics, 2021, PP.
   [1] HA J, PARK C. MLMD: Metric Learning for Predicting MiRNA-Disease Associations [J]. Ieee Access, 2021, 9: 78847-58.
   [1] DING Y, TIAN L-P, LEI X, et al. Variational graph auto-encoders for miRNA-disease association prediction [J]. Methods, 2020.

说明

2022和2021文章已经看完（2022还会持续更新，注意最新论文的状态即可）

2020年的文章看了一部分4篇。

至此，在写材料时，可减少对早期经典文章的引用，因为已经落伍了。