Table 1.
Comparison of ETNA with existing unsupervised pairwise network alignment methods.
| Method | Interpretable embeddings | Cross-species anchors | Combining sequence and topology | Directionality | Algorithm | Code availability |
|---|---|---|---|---|---|---|
| ETNA | Yes | Orthologs | Nonlinearly | Bidirectional | Autoencoders | Python |
| MUNK (Fan et al. 2019) | Yes | Orthologs | Nonlinearly | Directional | SVD | Python |
| IsoRank (Singh et al. 2008) | No | BLAST | Linearly | Bidirectional | PageRank | Linux executable |
| HubAlign (Hashemifar and Xu 2014) | No | BLAST | Linearly | Bidirectionala | Minimum-degree heuristic algorithm | C++ |
| PrimAlign (Kalecky and Cho 2018) | No | BLAST | Linearly | Bidirectional | Markov chain + PageRank | Not available |
| SANA (Mamano and Hayes 2017) | No | BLAST | Linearly | Bidirectionala | Simulated annealing | Webserver, C++ |
| L-GRAAL (Malod-Dognin and Pržulj 2015) | No | BLAST | Linearly | Bidirectional | Lagrangian graphlet | C++, not working |
| GHOST (Patro and Kingsford 2012) | No | GO | Does not use sequence | Bidirectionala | Seed-and-extend with local search | C++ |
| NETAL (Neyshabur et al. 2013) | No | GO | Does not use sequence | Bidirectionala | Greedy search on similarity matrix | Webserver |
| MAGNA++ (Vijayan et al. 2015) | No | n/a | Does not use sequence | Bidirectional | Genetic algorithm | Executable, C++ |
a
The method has a bidirectional objective function, but the returned output is directional.