Document-level phenotype concept recognition on ID-68
94.11PrecisionPhenoBERT
Evaluation results
| Method | Links | ||||
|---|---|---|---|---|---|
| PhenoBERTCategory=Neural2025.07 | 94.11 | 78.56 | 85.64 | 1 | |
| AutoPCRFTCategory=Prompt Based, LLM Backend=Qwen3-30B-A3B-Instruct-2507, Evaluation Protocol=Fine-tuned2025.07 | 88.77 | 77.05 | 82.49 | — | |
| NCBOCategory=Dictionary Based2025.07 | 88.75 | 64.69 | 74.84 | 7 | |
| FastHPOCRCategory=Dictionary Based2025.07 | 87.75 | 71.38 | 78.72 | 3 | |
| AutoPCRCategory=Prompt Based, LLM Backend=Qwen3-Next-80B-A3B-Instruct2025.07 | 84.33 | 76.71 | 80.34 | 2 | |
| PhenoTaggerCategory=Neural2025.07 | 84.16 | 72.38 | 77.83 | 5 | |
| OBOCategory=Dictionary Based2025.07 | 82.84 | 60.28 | 69.78 | 9 | |
| PhenoTagger++Category=Neural2025.07 | 79.81 | 72.76 | 76.12 | 6 | |
| NCRCategory=Neural2025.07 | 79.18 | 77.68 | 78.42 | 4 | |
| REALCategory=Prompt Based, LLM Backend=GPT-4o-mini2025.07 | 76.64 | 66.2 | 71.04 | 8 | |
| ClinPhenCategory=Dictionary Based2025.07 | 74.96 | 61.92 | 67.82 | 10 | |
| VanillaCategory=Prompt Based, LLM Backend=GPT-4o-mini2025.07 | 20.04 | 11.98 | 15 | 11 |