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  • Automated Annotation On Colonoscopy Reports (Poster)

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    AMIA
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    This document discusses automated annotation of colonoscopy reports to extract important clinical information. It aims to automatically classify variables like informed consent, adequate preparation, and whether the procedure was aborted from colonoscopy reports, which are often in free-text form. The researchers used machine learning techniques like decision trees to classify these variables from a dataset of over 450 colonoscopy reports. Evaluation metrics like precision, recall, and F1 score are reported to measure the performance of different classifiers for each variable. The best performing models are able to accurately extract many of the critical data elements from the free-text reports with high precision and recall.

    Originalbeschreibung:

    2013 Summit on Clinical Research Informatics

    Originaltitel

    Automated Annotation on Colonoscopy Reports (Poster)

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    This document discusses automated annotation of colonoscopy reports to extract important clinical information. It aims to automatically classify variables like informed consent, adequate preparation, and whether the procedure was aborted from colonoscopy reports, which are often in free-text form. The researchers used machine learning techniques like decision trees to classify these variables from a dataset of over 450 colonoscopy reports. Evaluation metrics like precision, recall, and F1 score are reported to measure the performance of different classifiers for each variable. The best performing models are able to accurately extract many of the critical data elements from the free-text reports with high precision and recall.

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    Attribution Non-Commercial (BY-NC)
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    36 Ansichten1 Seite

    Automated Annotation On Colonoscopy Reports (Poster)

    Hochgeladen von

    AMIA
    This document discusses automated annotation of colonoscopy reports to extract important clinical information. It aims to automatically classify variables like informed consent, adequate preparation, and whether the procedure was aborted from colonoscopy reports, which are often in free-text form. The researchers used machine learning techniques like decision trees to classify these variables from a dataset of over 450 colonoscopy reports. Evaluation metrics like precision, recall, and F1 score are reported to measure the performance of different classifiers for each variable. The best performing models are able to accurately extract many of the critical data elements from the free-text reports with high precision and recall.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Als PDF, TXT herunterladen oder online auf Scribd lesen
    Markieren Sie unangemessene Inhalte
    von 1

    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

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