Table 4.
Overview of Resource Allocation-Based Computational Methods for Inferring lncRNA-Disease Association
| Method Name | Computational Principle | Data Types | Available Tool (Package or Code) | References |
|---|---|---|---|---|
| BPLLDA | paths together with a decay function | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | NA | Xiao et al.51 |
| TPGLDA | resource allocation | disease-gene association, lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | code (https://github.com/USTC-HIlab/TPGLDA) | Ding et al.62 |
| IDHI-MIRW | positive pointwise mutual information, random walk with restart algorithm | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | IDHI-MIRW (https://github.com/NWPU-903PR/IDHI-MIRW) | Fan et al.50 |
| Lap-BiRWRHLDA | Laplacian normalization, random walks | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | NA | Wen et al.60 |
| IIRWR | random walk with restart algorithm | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | code (https://github.com/xiaoyubin123/code) | Wang et al.59 |
| LLCLPLDA | label propagation algorithm, locality-constrained linear coding | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | NA | Xie et al.55 |
| LION | network diffusion approach | lncRNA-protein interaction, protein-protein interaction, protein-disease interaction | NA | Sumathipala et al.53 |
| NBLDA | label propagation algorithm | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | NA | Liu et al.58 |
| DislncRF | random forest | RNA sequencing data, disease-protein coding gene association, lncRNA-disease association | code (https://github.com/xypan1232/DislncRF) | Pan et al.54 |
| NA | DeepWalk and a rule-based inference method | lncRNA-disease association, lncRNA-miRNA association, miRNA-disease association | code (https://github.com/Pengeace/lncRNA-disease-link) | Zhang et al.52 |
| NA | ncPred | disease-target association, target-ncRNA association, ncRNA-ncRNA association, target-target association | NA | Mori et al.63 |
| BiWalkLDA | Laplacian normalization, random walks | lncRNA-disease association, lncRNA-lncRNA association, disease-disease association | code (https://github.com/screamer/BiwalkLDA) | Gao et al.61 |
NA, not applicable.