Skip to main content

Table 5 Detailed accuracy metrics for the human annotator with respect to the ground truth (GT) in pathology reports. DCIS; ductal carcinoma in situ, LN; lymph nodes. All scores were computed by averaging the metrics across training and test cohorts

From: Automated medical chart review for breast cancer outcomes research: a novel natural language processing extraction system

Outcome Variable

Accuracy

Precision

Recall

F-Score

Invasive Carcinoma

0.98

1.00

0.98

0.99

Invasive Histologic Type

0.95

0.97

0.98

0.97

Nottingham Score

0.62

1.00

1.00

1.00

Glandular Differentiation

0.97

0.99

0.98

0.98

Nuclear Pleomorphism

0.97

0.98

0.98

0.98

Mitotic Rate

0.96

0.95

0.98

0.97

Histologic Grade

0.96

0.99

0.95

0.97

Tumour Size (mm)

0.98

0.96

0.98

0.97

Tumour Focality

0.96

0.97

0.98

0.97

# of Foci

0.96

0.98

0.97

0.97

Tumour Site

0.95

0.74

0.94

0.81

Lymphovascular Invasion

0.97

0.98

0.98

0.98

In situ Component

0.95

0.99

0.94

0.97

In situ Type

0.97

0.99

0.97

0.98

In situ Nuclear Grade

0.96

0.98

0.96

0.97

Necrosis

0.96

0.96

0.96

0.96

DCIS Extent

0.98

0.97

0.95

0.96

Architectural Patterns

0.96

0.93

0.95

0.94

Invasive Carcinoma Margins

0.96

0.97

0.98

0.97

Distance from Closest Margin

0.97

0.99

0.96

0.97

Closest Margin

0.97

1.00

0.96

0.98

DCIS Margins

0.94

0.94

0.97

0.95

Distance of DCIS from Closest Margin (mm)

0.95

0.99

0.94

0.96

Closest Margin DCIS

0.97

1.00

0.94

0.97

Total LN Examined

0.98

1.00

0.98

0.99

# Sentinel LN Examined

0.98

1.00

0.98

0.99

Micro/macro metastasis

0.98

1.00

0.98

0.99

# LN with Micro-metastasis

0.98

1.00

0.96

0.98

# LN with Macro-metastasis

0.98

1.00

0.96

0.98

Size of largest Macro-metastasis Deposit

0.98

1.00

0.95

0.98

Extranodal Extension

0.98

1.00

0.94

0.97

Extent (mm)

0.98

1.00

0.90

0.95

Invasive Tumour Size (mm)

0.97

1.00

0.97

0.98

# Sentinel Nodes Examined

0.96

0.96

0.96

0.96

# Micro-metastatic Nodes

0.98

1.00

0.95

0.98

# Macro-metastatic Nodes

0.97

1.00

0.93

0.96

Pathologic Stage

0.98

1.00

0.98

0.99

Overall

0.96

0.98

0.96

0.97