Table 3.

Micro and macro measurements for concept recognition experiments on 39 Undiagnosed Diseases Program clinical notes. Neural Concept Recognizer models were trained on Human Phenotype Ontology. Largest values for each category are italicized.

Method	Micro (%)			Macro (%)
	Precision	Recall	F1-score	Precision	Recall	F1-score
BioLarK	27.6	21.0	23.9	28.7	21.6	24.6
cTAKESa	31.5	18.9	23.6	37.5	20.2	26.2
OBOb	26.8	20.5	23.2	28.8	20.1	23.7
NCBOc	33.4	16.9	22.5	37.1	19.9	25.9
NCRd	24.5	27.2	25.8	26.5	27.6	27.0
NCR-He	25.1	26.8	25.9	26.2	27.0	26.6
NCR-Nf	24.3	28.5	26.2	27.0	28.9	27.9
NCR-HNg	25.5	27.2	26.4	27.4	27.7	27.6

^acTAKES: Clinical Text Analysis and Knowledge Extraction System.

^bOBO: Open Biological and Biomedical Ontologies 

^cNCBO: National Center for Biomedical Ontology.

^dNCR: Neural Concept Recognizer.

^eNCR-H: variation of the NCR model that ignores taxonomic relations.

^fNCR-N: variation of the NCR model that has not been trained on negative samples.

^gNCR-HN: variation of the NCR model that ignores the taxonomy and has not been trained on negative examples.