Models / bio-nlp / clinical-assertion-negation-bert / benchmarks

bio-nlp/clinical-assertion-negation-bert

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BC5CDR chemical NER bio-nlp/bc5cdr-chemical-ner

Drawn from: bc5cdr

atlas-n100-v1

Metric	Value	95% CI	n	Rank	Best in catalogue	Source	Overlap	Board
Chemical entity F1 (token probe) ↑ higher is better · probe	0.863	[0.823, 0.897]	100	5 / 16	0.889	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity precision (token probe) ↑ higher is better · probe	0.857	[0.807, 0.907]	100	5 / 16	0.870	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity recall (token probe) ↑ higher is better · probe	0.868	[0.825, 0.906]	100	6 / 16	0.914	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board

Clinical entity recognition (MACCROBAT) bio-nlp/clinical-entity-recognition

Drawn from: MACCROBAT_biomedical_ner

atlas-n100-v1

Metric	Value	95% CI	n	Rank	Best in catalogue	Source	Overlap	Board
Entity F1, 3 types (token probe) ↑ higher is better · probe	0.530	[0.462, 0.594]	100	4 / 16	0.724	reproduced	overlap Train/test overlap declared by the evaluator: PubMed Central full text	Board
Entity precision, 3 types (token probe) ↑ higher is better · probe	0.493	[0.426, 0.560]	100	4 / 16	0.709	reproduced	overlap Train/test overlap declared by the evaluator: PubMed Central full text	Board
Entity recall, 3 types (token probe) ↑ higher is better · probe	0.573	[0.504, 0.638]	100	4 / 16	0.739	reproduced	overlap Train/test overlap declared by the evaluator: PubMed Central full text	Board
Entity macro F1, 3 types (token probe) ↑ higher is better · probe · secondary	0.524	[0.443, 0.594]	100	—	0.728	reproduced	overlap Train/test overlap declared by the evaluator: PubMed Central full text	Board

PubMedQA accuracy bio-nlp/pubmedqa-accuracy

Drawn from: PubMedQA

atlas-full-v1

Metric	Value	95% CI	n	Rank	Best in catalogue	Source	Overlap	Board
Accuracy (logistic probe) ↑ higher is better · probe	0.548	[0.510, 0.588]	500	7 / 17	0.576	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Macro F1 (logistic probe) ↑ higher is better · probe	0.404	[0.359, 0.456]	500	5 / 17	0.444	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board

Spanish occupation entity recognition (ProfNER) bio-nlp/spanish-occupation-entity-recognition

Drawn from: ProfNER_corpus_NER

atlas-n100-v1

Metric	Value	95% CI	n	Rank	Best in catalogue	Source	Overlap	Board
Entity F1, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe	0.044	[0.000, 0.157]	100	14 / 16	0.630	reproduced	none declared	Board
Entity precision, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe	0.500	[0.000, 1.000]	100	12 / 16	1.000	reproduced	none declared	Board
Entity recall, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe	0.023	[0.000, 0.087]	100	13 / 16	0.535	reproduced	none declared	Board
Entity macro F1, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe · secondary	0.024	[0.000, 0.140]	100	—	0.329	reproduced	none declared	Board