TASK	DATASET	MODEL	METRIC NAME	METRIC VALUE	GLOBAL RANK
Named Entity Recognition (NER)	BC5CDR-chemical	NCBI_BERT(base) (P)	F1	93.5	# 10
Named Entity Recognition (NER)	BC5CDR-disease	NCBI_BERT(base) (P)	F1	86.6	# 4
Semantic Similarity	BIOSSES	NCBI_BERT(base) (P+M)	Pearson Correlation	0.9159999999999999	# 3
Relation Extraction	ChemProt	NCBI_BERT(large) (P)	F1	74.4	# 9
Medical Relation Extraction	DDI extraction 2013 corpus	NCBI_BERT(large) (P)	F1	79.9	# 2
Document Classification	HOC	NCBI_BERT(large) (P)	F1	87.3	# 2
Natural Language Inference	MedNLI	NCBI_BERT(base) (P+M)	F1	84	# 1
Semantic Similarity	MedSTS	NCBI_BERT(base) (P+M)	Pearson Correlation	0.848	# 1
Medical Named Entity Recognition	ShARe/CLEF eHealth corpus	NCBI_BERT(base) (P+M)	F1	0.792	# 3

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Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets

WS 2019 · Yifan Peng, Shankai Yan, Zhiyong Lu ·

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ncbi-nlp/NCBI_BERT official

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ncbi-nlp/BLUE_Benchmark official

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bigscience-workshop/biomedical

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gmpoli/electramed

Tasks

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Benchmarking

Document Classification

Drug–drug Interaction Extraction

Medical Named Entity Recognition

Medical Relation Extraction

Named Entity Recognition (NER)

Natural Language Inference

Relation Extraction

Semantic Similarity

Transfer Learning

Datasets

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BLUE

Used in the Paper:

GLUE

MIMIC-III

BC5CDR

DDI

BIOSSES

HOC ChemProt

MedNLI

Results from the Paper

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Ranked #1 on Semantic Similarity on MedSTS

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Task	Dataset	Model	Metric Name	Metric Value	Global Rank	Benchmark
Named Entity Recognition (NER)	BC5CDR-chemical	NCBI_BERT(base) (P)	F1	93.5	# 10	Compare
Named Entity Recognition (NER)	BC5CDR-disease	NCBI_BERT(base) (P)	F1	86.6	# 4	Compare
Semantic Similarity	BIOSSES	NCBI_BERT(base) (P+M)	Pearson Correlation	0.9159999999999999	# 3	Compare
Relation Extraction	ChemProt	NCBI_BERT(large) (P)	F1	74.4	# 9	Compare
Medical Relation Extraction	DDI extraction 2013 corpus	NCBI_BERT(large) (P)	F1	79.9	# 2	Compare
Document Classification	HOC	NCBI_BERT(large) (P)	F1	87.3	# 2	Compare
Natural Language Inference	MedNLI	NCBI_BERT(base) (P+M)	F1	84	# 1	Compare
Semantic Similarity	MedSTS	NCBI_BERT(base) (P+M)	Pearson Correlation	0.848	# 1	Compare
Medical Named Entity Recognition	ShARe/CLEF eHealth corpus	NCBI_BERT(base) (P+M)	F1	0.792	# 3	Compare

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Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets

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