Table 3.
Summary of computational methods for identifying missing HPO annotations
| Base | Method | Data source(s) | HPO hierarchy | Optimization |
|---|---|---|---|---|
| Label propagation | LP (Zhu et al. 2003; Zhou et al. 2003) | PPI | – | Closed-form solution |
| DLP (Petegrosso et al. 2017) | PPI | Raw HPO DAG | L-BFGS-B | |
| tlDLP (Petegrosso et al. 2017) | PPI, GO annotation | Raw HPO DAG | L-BFGS-B | |
| Matrix completion | SMC (Lee and Seung 2000) | – | – | ALS |
| AiProAnnotator (Gao et al. 2018) | PPI | Lin method | ALS | |
| HPOAnnotator (Gao et al. 2019) | Multiple PPIs | Lin method | ALS |