Applying Natural Language Processing in the Clinical Setting Peter Haug, MD Homer Warner Center for...

HL7

Applying Natural Language Processing in the Clinical Setting

Peter Haug, MDHomer Warner Center for Informatics ResearchIntermountain Healthcare, Salt Lake City, Utah

HL7

2

• Goals:

– Affect Care Delivery

• Extract Clinical Data from Medical

Documents

• Use Extracted Data to Alter Care

– Improve Documentation

• Identify Necessary Data

• Identify Eligible Patients

– Support Clinical Research

• Data Extraction

• Phenotype Recognition

• Research Alerting

– Improve Administrative Data

• Improve Data for Business Planning

• Improve Data for Billing

• Examples:

– Support for Diagnostic Systems

• Screening for Disease

• Assess Risk

• Triggering Orders

• Activating Clinical Protocols

– Encode Admit Diagnoses

– Identify Patients for Trauma Registry

– Complete Problem List

– Identify Patients for Research Recruitment

Applied NLP Research

HL7 Process Begins with a Document

Chest Xray Report

History: Cough and fever. Previous history of right-sided pneumonia.Exam: PA and Lateral Chest Film.Observations: Prior films showed confluent opacification of the RLL. This finding remains in today’s exam. These opacities, seen in multiple previous films, have spread to the right and left upper lobes. Interpretation: Extension of previously diagnosed pneumonia to right and left upper lobes.

•Find Document Structure

•Extract Meta-Data•Plan Further

Parsing•Find Sentence

Structure•Determine

Meaning (Concepts)

•Store/Process Concepts

Document Parsing Process

HL7

• Find Document Structure

• Find Section Structure

• Find Sentence Structure

• Determine Meaning (Semantics)

– Map to Concepts

– Build Data Structures

A Sequence of Processing

HL7Document Parsing Process

•Find Document Structure

•Extract Meta-Data•Plan Further



Meaning (Concepts)


Find Document Sections

Structured Document

Find Internal Structure

XML Based Output

<Doc>Chest Xray Report</Doc> <Sec>History</Sec> <Body> <Sen>Cough and fever.</Sen> <Sen>Previous history of right-sided pneumonia.</Sen> </Body> <Sec>Exam</Sec> <Body> <Sen>PA and Lateral Chest Film.</Sen> </Body> <Sec>Observations</Sec> <Body> <Sen>Prior films showed confluent opacification of the RLL.</Sen> <Sen>This finding remains in today’s exam.</Sen> <Sen>These opacities, seen in multiple previous films, have spread to the right and left upper lobes.</Sen> </Body> …………..</Doc>

Document

XML Based Output

<Doc>Chest Xray Report</Doc> <Sec>History</Sec> <Body>Cough and fever. Previous history of right-sided pneumonia.</Body> <Sec>Exam</Sec> <Body>PA and Lateral Chest Film. </Body> <Sec>Observations</Sec> <Body>Prior films showed confluent opacification of the RLL. This finding remains in today’s exam. These opacities, seen in multiple previous films, have spread to the right and left upper lobes. </Body> <Sec>Interpretation</Sec> ……………………..</Doc>

Ou

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Planner

Build Structures for:1) Document Type2) Sections3) Paragraphs4) Sentences

Choose Models to Parse Against:1) Rules to determine which group of concepts to find based on Document Type and Sections Present

Document Sections

5) Tables6) Internal Markup7) Images8) Lists

9) Images??

<Body>Prior films showed confluent opacification of the RLL. This finding remains in today’s exam. These opacities, seen in multiple previous films, have spread to the right and left upper lobes.</Body>

<Sen>These opacities, seen in multiple previous films, have spread to the right and left upper lobes.</Sen>

HL7 Planner

Choose Models to Parse Against:1) Rules to determine which group of concepts to find based on Document Type and Sections Present

•Find Structures•Extract Meta-Data•Plan Further



Meaning (Concepts)


Structured Data Storage

Sentences Determine Sentence Structure

Linked Phrasal Components

Determine Semantics

Output

XML Based Output

<Doc>Chest Xray Report</Doc> ………….. <Sec>Observations</Sec> <Body> <Sen><Coded Index=”1">Prior films showed confluent opacification of the RLL.</Coded></Sen> <Sen><Coded Index=”2">This finding remains in today’s exam.</Coded></Sen> <Sen><Coded Index=”3">These opacities, seen in multiple previous films, have spread to the right and left upper lobes.</Coded></Sen> </Body> …………..<Codes> <code ref=”1 Term=”Snomed”>2345</code> <code ref=”2 Term=”Snomed”>3456</code> <code ref=”3a Term=”Snomed”>1234</code> <code ref=”3b Term=”Snomed”>1235</code> …………..</Doc>

Data Base Storage

MetaData

Includes Document Type and Section Information.

Sen><Coded Index=”3">These opacities, seen in multiple previous films, have spread to the right and left upper lobes.</Coded></Sen>

<code ref=”3a” Terminology=”TermX?”>1234</code><code ref=”3b” Terminology=”TermX?”>1235</code>

Coded Findings:Localized Infiltrate-RULLocalized Infiltrate-LUL


Structured Document

HL7

•Categorize Words

• Identify Phrasal Boundaries

•Find Relationships Among Phrases

•Test for Semantic Congruence

•Extract Concepts

These opacities, seen in multiple views, have spread to the right and left upper lobes.

Lexicon: Derived from Specialist Lexicon?? And semantic KB

Identify Word

Properties

Sentence

these=>POS: Adj. Semantic Rep: N/Aopacities=>POS: Noun Num; Pleural Semantic Rep: RadFind.finding.opacities ID: 1seen=>POS: verb Num; N/A Semantic Rep: N/A ………………………...right=>POS: adj. POS: Noun Num; Singular Semantic Rep: RadFind.side.right ID: 2left=>POS: adj. POS: Noun Num; Singular Semantic Rep: RadFind.side.left ID: 3upper=>POS: adj. Num; N/A Semantic Rep: RadFind.sup_inf.upper ID: 4lobes=>POS: noun Num; pleural Semantic Rep: RadFind.anat_loc.lobes ID: 5Etc.

Ou

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Identify Candidate Phrases

Sentence/Word Properties

P1: these opacities: pntr- ID:1P2: in multipleP3: previous flimsP4: In multiple previous filmsP5: to the right: pntr- ID:2P6: to the left pntr- ID:3P7: upper lobes pntr- ID:4,5P8: to the right upper lobes pntr- ID:2,4,5P9: to the left upper lobes pntr- ID:3,4,5

Etc.

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Phrasal Grammar

Compositional Grammar

Phrasal Info

Etc.

Ou

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t

Phrasal Grammar

Semantic Restrictions

(ME&E Restrictions, Conjunctive Restrictions)

these opacities

to the right to the left

to the right upper lobes to the left upper

lobes

upper lobes

these opacities

these opacities

these opacities

these opacities

Sentence Parsing Process

these=>POS: Adj. Semantic Rep: N/Aopacities=>POS: Noun Num; Pleural Semantic Rep: RadFind.finding.opacities ID: 1seen=>POS: verb Num; N/A Semantic Rep: N/A ………………………...right=>POS: adj. POS: Noun Num; Singular Semantic Rep: RadFind.side.right ID: 2left=>POS: adj. POS: Noun Num; Singular Semantic Rep: RadFind.side.left ID: 3upper=>POS: adj. Num; N/A Semantic Rep: RadFind.sup_inf.upper ID: 4lobes=>POS: noun Num; pleural Semantic Rep: RadFind.anat_loc.lobes ID: 5Etc.

these opacities

to the left upper lobes

HL7

•Categorize Words

• Identify Phrasal Boundaries

•Find Relationships Among Phrases

•Test for Semantic Congruence

•Extract Concepts

These opacities, seen in multiple views, have spread to the right and left upper lobes.

Etc.

Compositional Grammar

Etc.

Outp

ut

Phrasal Grammar

these opacities

to the right to the left

to the right upper lobes to the left upper

lobes

upper lobes

these opacities

these opacities

these opacities

these opacities

Linked Phrasal ComponentsConcept

Extraction

s_anatomic_concept

c bilateral lungc heartc interpleural space ns c see previous eventc bilateral interpleural spacec nullc mediastinumc left lower lobec pulmonary vesselsc pleurac left upper lobec right lungc left interpleural spacec right lower lobec all thoracic locationsc left lungc bilateral lower lobesc right upper lobec right interpleural spacec aortaother-

16.09.568.935.494.744.504.464.353.002.842.732.572.572.492.252.211.901.781.621.5814.4

s_side

c nullc leftc rightc bilateralc either

61.413.810.611.3

2.77

s_superor_ inferior

c nullc upperc middlec lower

81.57.351.869.25

anatomic_modifier_side_

nullleftrightbilateralbothother-

61.413.610.57.822.813.83

anatomic_modifier_sup_ inf_

nulllowerupperbaseapicalother-

81.56.485.221.661.193.91

anatomic_ link_ term

nullinofatthroughoutother-

73.311.7

8.021.261.224.51

s_anatomic_ link_concept

c involvingc nullc throughoutc adjacent toc projecting onother-

86.58.344.070.750.120.20

anatomic_ location_modifier

nullotherwise advstructures ngeneralized adjremainder adjother-

93.00.710.400.360.285.22

anatomic_ location_term

nulllung nlobe npleural adjinterpleural adjheart nlungs ncardiac adjmediastinal adjchest nother-

16.215.78.958.317.125.775.424.033.082.4623.0

s_observations

c pneumothoraxc enlargement of the heartc abnormalityc ambiguityc lclzd prnchyml bnrmlty ns c generalized infiltratec localized infiltratec bilateral pleural effusionc nlrgmnt f th plmnry vsslsc generalized volume reducti...c parenchymal abnormality no c pulmonary nodular lesionc mediastinal wideningc pleural thickeningc generic infiltrate nos c pleural effusion ns c bony abnormalityc consolidation nos c localized volume reductionc vlm rfrnc t prvs rcrd other-

9.769.485.975.375.184.984.353.873.242.772.732.732.692.612.332.212.132.091.941.8621.7

s_ topic_concept

c enlargementc air densityc parenchymal abnormality ns c prly mrgntd pcty nfltrt c abnormalityc fluid densityc volume reductionc see previous eventc consolidationc smll wll mrgntd pcty ndl other-

12.711.510.69.178.737.944.784.193.993.5622.8

topic_ term

nullair nopacities nopacity nconsolidation nfluid ninfiltrate ninfiltrates neffusion nchanges nother-

22.310.36.325.854.033.643.322.652.251.9437.4

topic_modifier

nullnodular adjaccumulation nincreasedfocal adjhazy adjpatchy adjactive adjdegenerative adjlinear adjother-

79.31.981.661.581.300.670.590.510.510.5111.4

s_anatomic_concept


16.09.568.935.494.744.504.464.353.002.842.732.572.572.492.252.211.901.781.621.5814.4

s_side


61.413.810.611.3

2.77

s_superor_ inferior


81.57.351.869.25



61.413.610.57.822.813.83

anatomic_modifier_sup_ inf_


81.56.485.221.661.193.91

anatomic_ link_term


73.311.7

8.021.261.224.51

s_anatomic_ link_concept


86.58.344.070.750.120.20

anatomic_ location_modifier


93.00.710.400.360.285.22

anatomic_ location_term


16.215.78.958.317.125.775.424.033.082.4623.0

s_observations


9.769.485.975.375.184.984.353.873.242.772.732.732.692.612.332.212.132.091.941.8621.7

s_topic_concept


12.711.510.69.178.737.944.784.193.993.5622.8

topic_term


22.310.36.325.854.033.643.322.652.251.9437.4

topic_modifier


79.31.981.661.581.300.670.590.510.510.5111.4

s_ anatomic_ concept


16.09.568.935.494.744.504.464.353.002.842.732.572.572.492.252.211.901.781.621.5814.4

s_ side


61.413.810.611.3

2.77

s_ superor_ inferior


81.57.351.869.25

anatomic_ modifier_ side_


61.413.610.57.822.813.83

anatomic_ modifier_ sup_ inf_


81.56.485.221.661.193.91



73.311.7

8.021.261.224.51

s_ anatomic_ link_ concept


86.58.344.070.750.120.20

anatomic_ location_ modifier


93.00.710.400.360.285.22

anatomic_ location_ term


16.215.78.958.317.125.775.424.033.082.4623.0

s_ observations


9.769.485.975.375.184.984.353.873.242.772.732.732.692.612.332.212.132.091.941.8621.7

s_ topic_ concept


12.711.510.69.178.737.944.784.193.993.5622.8

topic_ term


22.310.36.325.854.033.643.322.652.251.9437.4

topic_ modifier


79.31.981.661.581.300.670.590.510.510.5111.4

s_ anatomic_ concept


16.09.568.935.494.744.504.464.353.002.842.732.572.572.492.252.211.901.781.621.5814.4

s_ side


61.413.810.611.3

2.77

s_ superor_ inferior


81.57.351.869.25

anatomic_ modifier_ side_


61.413.610.57.822.813.83

anatomic_ modifier_ sup_ inf_


81.56.485.221.661.193.91



73.311.7

8.021.261.224.51

s_ anatomic_ link_ concept


86.58.344.070.750.120.20

anatomic_ location_ modifier


93.00.710.400.360.285.22

anatomic_ location_ term


16.215.78.958.317.125.775.424.033.082.4623.0

s_ observations


9.769.485.975.375.184.984.353.873.242.772.732.732.692.612.332.212.132.091.941.8621.7

s_ topic_ concept


12.711.510.69.178.737.944.784.193.993.5622.8

topic_ term


22.310.36.325.854.033.643.322.652.251.9437.4

topic_ modifier


79.31.981.661.581.300.670.590.510.510.5111.4

Semantic Tests1) Model determines Semantic consistency of phrasal combinations.2) “Best” combinations trigger concept extraction and storage.

Structured Data

Storage

Data Base Storage


From Words to Coded Findings:Localized Infiltrate-RULLocalized Infiltrate-LULthese opacities

to the left upper lobes

HL7 Output of a Semantic Parse

• Instantiated Event:• 1001 *Overall Concept : *localized infiltrate (0.998669)• 1002 *State Concept : *present (0.780993)• 1003 Presence Term : null (0.779583)• 1004 *Topic Concept : *poorly-marginated opacity (infiltrate) (1.0)• 1005 Topic Term : opacity~n (1.0)• 1006 Topic Modifier Term: hazy~adj. (1.0)• 1008 Topographic Location Term : null (0.588844)• 1009 *Severity Concept : *null (0.969009)• 1010 Severity Term : null (0.962739)• 1011 *Link Concept : involving (0.686011)• 1012 Topic Location Link Term : in (1.0)• 1013 *Anatomic Concept : *right upper lobe (1.0)• 1014 Anatomic Location Mod : null (0.9375)• 1015 Anatomic Location : lobe~n (1.0)• 1016 Anatomic Location Mod1 : right (1.0)• 1017 Anatomic Location Mod2 : upper (1.0)• 1018 Anatomic Location Mod3 : null (1.0)• 1019 Anatomic Location Mod4 : null (1.0)• 1020 Anatomic Location Mod5 : null (1.0)

• Instantiated Event:• 1001 *Overall Concept : *localized infiltrate (0.998669)• 1002 *State Concept : *present (0.780993)• 1003 Presence Term : null (0.779583)• 1004 *Topic Concept : *poorly-marginated opacity (infiltrate) (1.0)• 1005 Topic Term : opacity~n (1.0)• 1006 Topic Modifier Term: hazy~adj. (1.0)• 1008 Topographic Location Term : null (0.588844)• 1009 *Severity Concept : *null (0.969009)• 1010 Severity Term : null (0.962739)• 1011 *Link Concept : involving (0.686011)• 1012 Topic Location Link Term : in (1.0)• 1013 *Anatomic Concept : *right upper lobe (1.0)• 1014 Anatomic Location Mod : null (0.9375)• 1015 Anatomic Location : lobe~n (1.0)• 1016 Anatomic Location Mod1 : right (1.0)• 1017 Anatomic Location Mod2 : upper (1.0)• 1018 Anatomic Location Mod3 : null (1.0)• 1019 Anatomic Location Mod4 : null (1.0)• 1020 Anatomic Location Mod5 : null (1.0)

PARSE: A hazy opacity is seen in the right upper lobe.

HL7 Probabilistic Semantics

Locationbilateral lungleft lower lobenullbilateral lower lobesleft upper lobeother-

26.514.010.18.177.3933.9

GlobalObservationabnormalitylocalized infiltratealveolar infiltrate nosgeneric infiltrate nos

0 +58.414.826.8

topic_term

abcessabnormalitiesconsolidationinfiltratesopacityvisualizationinfiltrateopacificationopacitiesdensitiesconsolidatedair bronchogramkerley linesseptal lineschangeslesionnullairchangedensity

.002

.00231.118.310.50.3930.70.392.730.390.390.390.390.391.170.390.390.390.391.17

Stateabsentpresentpossibleotherwise absent

28.864.26.620.39

Observationlocalized infiltrateinfiltrate nosgeneralized infiltrateinterstitial infiltrateinflammatory lesionother-

53.343.21.950.780.390.39

topic_modifier

nullfocalsuperimposedhazymildly coarse patternconfluentinfiltrativemixed patterndensepatchyareas ofareareticularnodularinflammatoryill definedindistinctpoorly marginatedslightly coarsebronchogramunderlyingfluffyill defined poorly definedvague

69.66.610.393.500.390.783.110.391.561.950.780.390.390.780.380.781.171.170.390.390.391.951.950.390.39

anatomic_location_term

pulmonarynulllunglungshemithoraxlobesperivascularlobelung fieldschestlocationinfrahilarsideheartretrocardiaclingula

3.5137.715.53.890.783.890.4028.40.400.400.400.390.401.170.781.95

Modifier_Side

nullleftrightbilateraleither

52.921.816.38.570.40


nulleitherrightbilaterallyleftbilateralboth

52.50.4016.30.7822.23.504.28

Modifier_Sup_Inf

nullascendingdescendingsuperiormiddleinferior

58.7.007.00711.72.7326.8

anatomic_modifier_sup_inf_

nulllowerupperbaseapexcranialbasesmidbasilarmiddle

58.722.610.91.950.390.391.561.170.781.56

Modifier_Cntrl_Prph_

nullcentralperipheral

97.31.950.79

anatomic_mdfr_cntrl_prph_

nullperipheralcentralperipherally

97.30.391.950.39

state_term

nullnono evidencewith noorparticularlywithoutpossiblyand ormost likelyother-

62.318.74.674.282.331.560.780.780.780.783.12

HL7• Goal:

– Identify Pneumonia Patients in the ED Rapidly– Assess Risk– Suggest Intervention

• Approach:– Use Probabilistic System to Identify Patients– Suggest Enrollment in Pneumonia Protocol– Provide Therapeutic Suggestions

• Requires Data Extracted from the X-ray Report

Example: NLP in Pneumonia(a computer-based intervention)

HL7 Care Delivery Framework

Pneumonia Screening Tool

Data Supporting Pneumonia Assessment Clinical Data

Repository

Pneumonia Guideline

Enrollment

Pneumonia Treatment Protocol

Computable Medical Knowledge Reposotory

Chest Xray Reports

Chest Xray Report Processing

(Structured Data Extraction)

Example: Community-Acquired Pneumonia

HL7



Repository

Pneumonia Guideline

Enrollment



Chest Xray Reports



Care Delivery Framework


Does the patient have pneumonia?

HL7



Repository

Pneumonia Guideline

Enrollment



Chest Xray Reports






Should we used the guideline?

HL7



Repository

Pneumonia Guideline

Enrollment



Chest Xray Reports






Should we used the guideline?

Apply Pneumonia Care Protocol.

HL7

• Web Services Infrastructure

• A Bayesian Network

• Supported by a Production Rules System

(DROOLS)

• Using an NLP System

– Sentence Isolation

– Random Forests-Based Semantics

Implimented Using:BPDiastolic

< 69.569.5 to 82.5>= 82.5

28.336.235.5

76.9 ± 11

Chloride

< 103.5103.5 to 105.5>= 105.5

42.125.132.9

104.3 ± 1.8

WBC

< 11.8511.85 to 18.75>= 18.75

86.112.41.45

9.46 ± 3.4

PNEUMONIAAbsentPresent

94.95.09

Age

< 15.515.5 to 45.5>= 45.5

8.0645.646.4

42 ± 21

RespRate

< 19.519.5 to 21.521.5 to 27.5>= 27.5

52.324.916.16.72

20.8 ± 3.5

TempC

< 36.7536.75 to 37.4537.45 to 38.05>= 38.05

62.723.86.047.46

36.79 ± 0.63

MeanBP

< 85.585.5 to 99.5>= 99.5

23.035.441.7

95.1 ± 12

BPSystolic

< 121.5121.5 to 148.5>= 148.5

29.444.626.0

134 ± 22

HeartRate

< 85.585.5 to 99.599.5 to 110.5>= 110.5

44.524.713.017.8

92.1 ± 15

Sodium

< 137.5137.5 to 140.5>= 140.5

25.741.832.6

139.2 ± 2.4

BUN

< 13.5>= 13.5

45.154.9

Creatinine

< 0.405>= 0.405

3.9096.1

SpO2

< 92.192.1 to 95.395.3 to 98.4>= 98.4

10.223.644.921.3

96.1 ± 3

BS_CONGESTION

YesNo

0.5399.5

BS_RHONCHI

YesNo

0.4399.6

BS_ABNORMAL

YesNo

3.8796.1

BS_DECREASED

YesNo

2.2997.7

BS_COURSE

YesNo

0.9099.1

BS_WHEEZES

YesNo

2.8497.2

BS_NO_COUGH

YesNo

0 + 100

BS_STRIDOR

YesNo

.08399.9

BS_CLEAR

YesNo

44.056.0

BS_CRACKLES

YesNo

0.7299.3

BS_RALES

YesNo

0.1199.9

BS_ABSENT

YesNo

.030 100

BS_INSPIRATION

YesNo

0.7999.2

BS_TUBULAR

YesNo

.024 100

BS_INFREQUENT

YesNo

0.6299.4

BS_STRONG

YesNo

0.7699.2

BS_FINE_CRACK...

YesNo

0.3199.7

BS_EXPIRATION

YesNo

0.9099.1

BS_NOT_CLEARING_SECREA...

YesNo

0.1099.9

BS_FREQUENT

YesNo

1.1998.8

BS_WEAK

YesNo

0.1699.8

BS_NON_PRODUCTIVE_CO...

YesNo

1.7498.3

BS_PRODUCTIVE_CO...

YesNo

1.8198.2

BS_MODERATE

YesNo

1.3698.6

BS_CLEARING_SECREA...

YesNo

0.4599.6

ChiefComplaint

RESPIRATORY COMPLAINTFEVERABD PAINORTHO INJURYCHEST PAINNEURO COMPLAINTFALLTRAFFIC INJURYABD PROBLEMSCHEST PRESSUREBACK PAINWEAKNESSSYNCOPEENT PROBLEMBODY ACHESCV COMPLAINTSHEADACHEDIZZYFLANK PAINCV PROBLEMSASSAULT RAPEPSYCHIATRICCHEST HEAVINESSSKIN COMPLAINTSPECIFIC DIAGNOSISDIABETICPAIN CHESTHEART RACETRAUMAGENITOURINARY PROBLEMPALPITATIONSHEART IRRALLERGIESHIGH BPFLUID NUTRITIONCONVULSIONSINFECTIONRAPID HRIRR HEARTBEATLACERATIONINGESTIONBP HIGHUNCONSCIOUSNESSVAGINAL BLEEDINGMED REFILLUNKNOWNLOW BPCARDIAC ARRESTEYE PROBLEMBP LOWother-

32.46.966.054.264.123.693.623.503.453.102.822.792.282.191.881.881.831.771.430.920.870.860.820.780.510.440.370.330.310.310.310.300.290.280.270.250.200.190.160.160.160.130.11.098.091.087.064.059.055.0540.18

NLP_FINDINGPositiveNegative

25.974.1

HL7 Patient Tracking Board

HL7 Patient Tracking Board

HL7

HL7

HL7

• Natural Language Processing Does Play A Role In Patient Care

• Useful Applications Will Blend NLP-Derived Data With Structured Data From The EHR

• Radiology Reports Are A Data-rich Target For NLP

Conclusion

HL7

23

Questions???

Date post:	19-Jan-2016
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