Table 2 Summary of graph embedding on biomedical data
From: Graph embedding on mass spectrometry- and sequencing-based biomedical data
Techniques | Dataset | Applications | Evaluation Metrics |
|---|---|---|---|
Combined DeepWalk, LINE, Node2vec, and SDNE [26] | MATADOR, PubTator, and BioGRID | Link prediction | AUC, AUPR, MAP, Avg. R-precision, and Precision@k |
HeteWalk [115] | HPRD, MISIM, MimMiner, DisGeNET, and miRTarBase | Link prediction | AUC |
Cascade model [97] | BioChem, Drug Bank, and PubChem | Link prediction | Accuracy, hits@10, and AUC |
[29] | Krogan, Dip, and BioGRID | Node clustering | Precision, recall, F-score, fraction, geometry accuracy, and MMR |
HNERMDA [102] | MDAD and aBiofilm | Link prediction | Accuracy, AUC, and AUPR |
PmDNE [30] | HMDD3.0 | Link prediction | AUC, AUPR, precision, accuracy, recall, and F1-score |
HO-VGAE [27] | HI-II-14, HI-III, Lit-BM-13, BioGRID, and Bioplex | Link prediction | AUPR, Precision@k |
HMNE [105] | Lazega, CKM, DBLP, C.elegans, H.genetic, PPI, and Twitter | Link prediction and node classification | F1-micro, F1-macro, and AUC |
TriModel [99] | DrugBank_FDA, KEGG_MED, and Yamanishi_08 | Link prediction | AUC and AUPR |
FactorHNE [103] | DisGeNet, HPO and Orphanet, STRING 10 | Link prediction | AUPR, AUC, Precision@K, and Recall@K |
[100] | DrugBank_FDA, UNIPROT | Link prediction, node clustering | Accuracy |
Hybrid model GVS [31] | GO, HPRD, CTD, HMDD and MATADOR | Link prediction | Accuracy and F1-score |
DeepWalk and Node2vec [98] | DrugBank, Bio2RDF, human disease network, SIDER, KEGG, and PharmGKB | Link prediction | AUC and AUPR |
Netpro2vec [92] | LFR, MREG, Kidney RNASeq, Brain fMRI COBRE, Breast RNAseq, Breast Microarray, MUTAG | Node classification | Accuracy, precision, recall, F-score, and MCC |
BiLSTM [101] | Human, DUD-E, and ChEMBL | Node classification | AUC, precision, and recall |
scLINE [104] | Usoskin, Li, Pollen, Patel, Darmanis, Camp, Muraro, and Petropoulos | Node clustering | DBI, NMI, ARI, Jaccard and Purity |
PRD [34] | Bio2RDF, and DDI Corpus | Link prediction | AUC, AUPR |
ACNE and ACNE-ST [116] | Cora, Citeseer, Wiki, and DBLP_C4 | Node classification and node clustering | F1-micro and F1-macro |
Pathway2vec [33] | EcoCyc, HumanCyc, AraCyc, YeastCyc, LeishCyc, and TrypanoCyc | Link prediction and node clustering | F1-micro |
LPPI [28] | PPI network and GraphSAGE-PPI | Link prediction and Node Classification | Accuracy, sensitivity, precision, MCC, and AUC |
MRMTI [32] | miRTarBase, miRBase, HumanNet, and biomaRt | Link prediction | AUC, AUPR, precision, recall, F1-score, and balanced accuracy |
CANE [117] | Disease Encylopedia Section of XYWY.com. | Link prediction | Precision@k and recall@k |