Models / bio-nlp / biobert-base-cased-v1-2 / benchmarks

bio-nlp/biobert-base-cased-v1-2

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bc5cdr bio-nlp/bc5cdr

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	0.878	[0.845, 0.912]	100	2 / 16	0.889	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity precision (token probe) ↑ higher is better · probe	0.870 best	[0.825, 0.916]	100	1 / 16	0.870	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity recall (token probe) ↑ higher is better · probe	0.885	[0.852, 0.915]	100	4 / 16	0.914	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board

MACCROBAT_biomedical_ner bio-nlp/maccrobat-biomedical-ner

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	0.504	[0.431, 0.569]	100	7 / 16	0.724	reproduced	unknown	Board
Entity precision, 3 types (token probe) ↑ higher is better · probe	0.474	[0.403, 0.542]	100	6 / 16	0.709	reproduced	unknown	Board
Entity recall, 3 types (token probe) ↑ higher is better · probe	0.538	[0.461, 0.609]	100	7 / 16	0.739	reproduced	unknown	Board
Entity macro F1, 3 types (token probe) ↑ higher is better · probe · secondary	0.489	[0.404, 0.564]	100	—	0.728	reproduced	unknown	Board

ProfNER_corpus_NER bio-nlp/profner-corpus-ner

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	0.083	[0.000, 0.189]	100	12 / 16	0.630	reproduced	none declared	Board
Entity precision, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe	0.400	[0.000, 1.000]	100	15 / 16	1.000	reproduced	none declared	Board
Entity recall, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe	0.047	[0.000, 0.114]	100	12 / 16	0.535	reproduced	none declared	Board
Entity macro F1, PROFESION + SITUACION_LABORAL (token probe) ↑ higher is better · probe · secondary	0.044	[0.000, 0.178]	100	—	0.329	reproduced	none declared	Board

PubMedQA bio-nlp/pubmedqa

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	0.562	[0.526, 0.598]	500	3 / 17	0.576	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Macro F1 (logistic probe) ↑ higher is better · probe	0.410	[0.367, 0.456]	500	3 / 17	0.444	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board