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Automated Annotation on Colonoscopy Reports

1
Pham ,

1
PhD ,

1
PhD ,

Phuong
Janyce Wiebe,
Rebecca Hwa,
Wendy W Chapman,
1University of Pittsburgh, Pittsburgh, PA; 2University of California, San Diego, CA

Electronic
Health
Record

Clinical research

automatic extract
important information

2
PhD

Colonoscopy
report
A transforming rule from Variables to Indicators

Data-driven
quality measures

Is there a
nursing report?
Yes

No

free-text form

Not eligible

Was informed
consent obtained?
Yes

Pass

No

Eligible

Yes class performance: Predict as -> No

Record yes if physician stopped the procedure early


due to too much stool, patient discomfort, etc.
proc-aborted definition

Variable
any-adenoma
appendiceal-orifice
ASA
Biopsy
Cecum
ileo-cecal-valve
indication-type
informed-consent
nursing-report
prep-adequate-YES
prep-adequate-NO
prep-adequateNOTMENTIONED
proc-aborted
withdraw-time

Yes

No
128
288
407
75
445
306
22
289
27
225
38

325
165
46
378
8
147
431
164
426
228
415

Yes %
28.26%
63.58%
89.85%
16.56%
98.23%
67.55%
4.86%
63.80%
5.96%
49.67%
8.39%

190

265

41.76%

6
450

447
3

1.32%
99.34%

Variable
any-adenoma
appendiceal-orifice
ASA
Biopsy
Cecum
ileo-cecal-valve
indication-type
informed-consent
nursing-report
prep-adequate-NO
prep-adequateNOTMENTIONED
prep-adequate-YES
proc-aborted
withdraw-time

P
95.4
98.1
98.5
42.8
98.9
98.6
85.7
99.2
88.9
57.1

C-QUAL
R
F
97.7 96.5
87.2 92.3
99.5 99.0
98.7 59.7
98.7 98.8
89.5 93.8
81.8 83.7
81.0 89.1
59.3 71.1
21.1 30.8

SimpleSQ
P
R
F
95.4 97.7 96.5
96.8 83.0 89.4
100 99.5 99.8
42.5 60.0 49.7
98.8 89.9 94.1
98.0 94.8 96.4
73.3 100 84.6
97.0 88.2 92.4
85.7 22.2 35.3
92.9 34.2 50.0

J48-no sampling
P
R
F
95.3 94.9 95.1
91.1 93.4 92.2
99.9 99.5 99.6
70.7 61.8 65.9
98.2 99.4 98.8
96.0 96.5 96.2
76.7 77.7 77.1
98.2 98.6 98.4
78.5 84.8 81.5
60.6 44.8 51.2

J48-down sampling
P
R
F
99.6 94.1
96.8*
79.2 90.2
84.3*
93.1 89.6
91.2*
89.4 80.2
84.5*
NaN 0.0
NaN
79.3 93.7
85.8*
25.1 55.3
34.1*
88.9 94.7
91.7*
34.3 72.4
46.2*
38.6 47.3
41.6*

80.9

95.8

87.7

69.3

82.1

75.2

86.6

87.8

87.2

86.9

90.5

88.7*

95.3
0.0
100

90.7
0.0
99.8

92.9
NaN
99.9

78.0
2.0
100

74.2
33.3
100

76.1
3.9
100

84.2
NaN
99.5

85.6
0.0
99.8

84.9
NaN
99.6

9.2
NaN
NaN

1.2
0.0
0.0

2.1*
NaN
NaN

Yes

No class performance: Predict as -> No

Yes

No

TN

FP

No

TP

FN

Yes

FN

TP

Yes

FP

TN