From: Ontology-driven and weakly supervised rare disease identification from clinical notes
validation (n=142+/400) | test (n=187+/673) | test, seen in WS (n=80+/499) i.e. both rules [not] satisfied | test, unseen in WS (n=107+/174) i.e. only one rule satisfied | |||||||||
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Text to UMLS | P | R | \(F_{1}\) | P | R | \(F_{1}\) | P | R | \(F_1\) | P | R | \(F_1\) |
SemEHR [15] | 35.5 | 100.0 | 52.4 | 27.8 | 100.0 | 43.5 | 16.0 | 100.0 | 27.6 | 61.5 | 100.0 | 76.2 |
+ rules | 80.9 | 89.4 | 84.9 | 68.6 | 94.7 | 79.6 | 83.3 | 87.5 | 85.4 | 61.5 | 100.0 | 76.2 |
+ WS (rules+BERT) | 92.0 | 89.4 | 90.7 | 81.4 | 91.4 | 86.1 | 83.3 | 87.5 | 85.4 | 80.2 | 94.4 | 86.7 |
+ SS (anns+BERT) | - | - | - | 88.4 | 93.6 | 90.9 | 87.7 | 88.8 | 88.2 | 88.9 | 97.2 | 92.9 |