Biomedical Entity Linking on NCBI
92.8Acc@1GenBioEL + ANGEL_PT+FT
Evaluation results
| Method | Links | ||
|---|---|---|---|
| GenBioEL + ANGEL_PT+FTBackbone=GenBioEL, Protocol=pre-training and fine-tuning2024.08 | 92.8 | — | |
| GenBioEL + ANGEL_FTBackbone=GenBioEL, Protocol=fine-tuning2024.08 | 92.5 | — | |
| ResCNNModel Category=Similarity-based BioEL & Re-ranking2024.08 | 92.4 | — | |
| SapBERTModel Category=Similarity-based BioEL & Re-ranking2024.08 | 92.3 | — | |
| SapBERTBackbone=SapBERT, Mirror-tuning=false2021.04 | 92 | 95.6 | |
| Prompt-BioELModel Category=Similarity-based BioEL & Re-ranking2024.08 | 91.9 | — | |
| GenBioELSource=reported, Model Category=Generative BioEL2024.08 | 91.9 | — | |
| BioBART + ANGEL_FTBackbone=BioBART, Protocol=fine-tuning2024.08 | 91.9 | — | |
| BART + ANGEL_FTBackbone=BART, Protocol=fine-tuning2024.08 | 91.4 | — | |
| KRISSBERTModel Category=Similarity-based BioEL & Re-ranking2024.08 | 91.3 | — | |
| BioSYNModel Category=Similarity-based BioEL & Re-ranking2024.08 | 91.1 | — | |
| GenBioELSource=reproduced, Model Category=Generative BioEL2024.08 | 91 | — | |
| Mirror-BERTBackbone=PubMedBERT, Mirror-tuning=true2021.04 | 90.9 | 94.8 | |
| BARTSource=reproduced, Model Category=Generative BioEL2024.08 | 90.3 | — | |
| BARTSource=reported, Model Category=Generative BioEL2024.08 | 90.2 | — | |
| BioBARTSource=reported, Model Category=Generative BioEL2024.08 | 89.9 | — | |
| BioBARTSource=reproduced, Model Category=Generative BioEL2024.08 | 89.4 | — | |
| Mirror-BERTBackbone=BERT, Mirror-tuning=true2021.04 | 87.2 | 92.1 | |
| PubMedBERTBackbone=PubMedBERT, Mirror-tuning=false2021.04 | 77.8 | 86.9 | |
| BERTBackbone=BERT, Mirror-tuning=false2021.04 | 67.6 | 77 |