Table 3 Results of our named entity evaluation using Bio_ClinicalBERT

		Scoring strategy
		Strict			Relaxed
Category	# In test set	P	R	F1	P	R	F1
Acute substance use	141	0.67	0.62	0.64	0.73	0.66	0.69
Aggressive behavior	263	0.63	0.71	0.67	0.67	0.77	0.72
Cognition	627	0.69	0.73	0.71	0.72	0.78	0.75
High utilization or incarceration	92	0.69	0.66	0.67	0.72	0.69	0.7
Mood symptoms	139	0.62	0.66	0.64	0.66	0.71	0.68
Noncompliance	228	0.64	0.65	0.64	0.69	0.7	0.69
Psychosis	66	0.63	0.73	0.68	0.67	0.77	0.72
Unmet needs or conflict	175	0.43	0.45	0.44	0.47	0.5	0.48
Total (micro avg.)	1463	0.64	0.67	0.65	0.68	0.72	0.7

Strict scoring requires exact matching of start and end character indices and category, while relaxed scoring requires category matching and half or more of gold and predicted tokens to overlap.

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