Models / bio-nlp / sapbert-from-pubmedbert-fulltext / benchmarks

bio-nlp/sapbert-from-pubmedbert-fulltext

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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	0.655	[0.591, 0.719]	100	16 / 16	0.889	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity precision (token probe) ↑ higher is better · probe	0.589	[0.506, 0.685]	100	16 / 16	0.870	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Chemical entity recall (token probe) ↑ higher is better · probe	0.738	[0.676, 0.794]	100	14 / 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	0.381	[0.302, 0.464]	100	16 / 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	0.394	[0.314, 0.485]	100	15 / 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	0.368	[0.276, 0.468]	100	16 / 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	0.401	[0.317, 0.477]	100	—	0.728	reproduced	overlap Train/test overlap declared by the evaluator: PubMed Central full text	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	0.044	[0.000, 0.148]	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, 0.083]	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, 0.130]	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	0.532	[0.492, 0.572]	500	10 / 17	0.576	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board
Macro F1 (logistic probe) ↑ higher is better · probe	0.398	[0.351, 0.446]	500	7 / 17	0.444	reproduced	overlap Train/test overlap declared by the evaluator: PubMed abstracts	Board