Table 5.
Exemplifying results for Experiment II: Top twelve ranked candidate terms (highest cosine similarity) from the word embeddings created with CBOW and Skip-gram using two terms as target: “OLR1” from the abstract of the PubMed article with ID = 22,738,689; and “oxidized_low-density_lipoprotein receptor_ 1” that is the CVDO protein class name (rdfs:label) for the CVDO class gene with name (rdfs:label) OLR1. Hence, the target term exploits the protein class expressions within the CVDO
| CBOW | Skip-gram | |||
|---|---|---|---|---|
| Rank | Candidate terms from word embeddings | Cosine | Candidate terms from word embeddings | Cosine |
| 1 | atherogenesis | 0.469405 | lectin-like_oxidized_low-density_lipoprotein | 0.688603 |
| 2 | atherosclerosis | 0.465861 | (LOX-1)_is | 0.672042 |
| 3 | CD36 | 0.439280 | atherosclerosis_we_investigated | 0.669050 |
| 4 | LOX-1 | 0.424173 | receptor-1 | 0.664891 |
| 5 | atherosclerotic_lesion_formation | 0.416537 | lectin-like_oxidized_LDL_receptor-1 | 0.663988 |
| 6 | vascular_inflammation | 0.414620 | lOX-1_is | 0.660110 |
| 7 | inflammatory_genes | 0.411186 | human_atherosclerotic_lesions | 0.657075 |
| 8 | atherosclerotic_lesions | 0.405906 | oxidized_low-density_lipoprotein_(ox-LDL) | 0.655515 |
| 9 | monocyte_chemoattractant_protein-1 | 0.398739 | oxidized_low-density_lipoprotein_(oxLDL) | 0.654965 |
| 10 | plaque_destabilization | 0.398201 | (LOX-1) | 0.652099 |
| 11 | oxidized_low-density_lipoprotein_(oxLDL) | 0.397967 | proatherosclerotic | 0.651571 |
| 12 | atherosclerosis_atherosclerosis | 0.396677 | receptor-1_(LOX-1)_is | 0.649000 |