Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory...

Pooyan AsgariUniversity of Sydney , School of ITHealth Information Technologies Research LaboratorySupervisor : Professor Jon PatrickSupervisor : Professor Jon Patrick

Pooyan AsgariUniversity of Sydney , School of ITHealth Information Technologies Research LaboratorySupervisor : Professor Jon PatrickSupervisor : Professor Jon Patrick

A noise prone environment : a noisy environment Even low level of the noise can effectively affect the

process of the content.

Developing a tool for identifying clinical terms and concepts within a noise prone collection of clinical notes has its own requirements and issues.

Clinical notes are example of the Noise prone environment

The ultimate goal is to identifying co-morbidities with obesity.

2

Discharge Date: 6/26/1990 HISTORY OF PRESENT ILLNESS: This is a 37 year old female who has had pain in her old appendectomy incision. The patient has had pain intermittently in the right lower quadrant in the old appendectomy scar for many years. She denies nausea or vomiting , or history of intestinal obstruction. Family History : not obese , no evidence Family History : not obese , no evidence

of cancer or CHFof cancer or CHF. Diabetes .Diabetes . PAST MEDICAL HISTORY: significant for

hypertension? . She had an appendectomy in 1965. She had a right carpal tunnel release in

1985 , and a right wrist tendon surgery in 1987. She has chronic obstructive pulmonary disease. MEDICATIONS ON ADMISSION: Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies. ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES

NAUSEA AND VOMITING. She does not smoke and only occasionally drinks.

REVIEW OF SYSTEMS: No evidence for : hypertension , CAD.

PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate is 80. In general , this is an overweight , otherwise were 2+ in the radial and dorsalis pedis. Abdomen: Soft ,

obese , nontender , with some mild incisional tenderness over the area of the appendectomy scar. Neurological examination was nonfocal.

HOSPITAL COURSE: The patient was taken to the operating room on 8/6/90 . The procedure performed was anincisional hernia repair by Dr. Cartmill and Dr. Borza . The patient tolerated the procedure well and was returned to the floor that evening. Since that time , the patient has had been somewhat slowto mobilize. She has complained of some nausea and some pain in the abdomen. She was given a PCA pump for the pain. The patientShe had slow ambulating despite the PCA pump , but was felt by Dr. Kabel that the patient would continue to improve , and we could increase the p.o. medications and switch to a plan for discharge tomorrow.DISPOSITION: She was discharged on the following medications:Percocet one to two p.o. q4-6 hours ,

Hydrochlorothiazide 20 mg p.o. q-day were the extent of hermedications. FOLLOWUP: She is to be followed in the office by Dr. Serles as an outpatient.

3Identifying clinical concepts in a

noise prone environment

The first common issue comes from a scattered matrix of evidence for a specific or rare concept . (e.g. CHF and Heart Failure)

Considering more features or patterns Advantages : Hope of covering more rare

situations Disadvantages : May lead to the absorption of

more noise by the system and impact the identification of other major terms and concepts, and therefore the overall performance of the system.



The Second common issue comes from the nature of the data collection & the necessary process for gathering evidence about Existence/Absent of a specific search concept .

Assuming 4 possible answers for a search concept: 1. Yes/Exists : There is enough positive evidence 2. No/ Not Exists :There is enough negative evidence 3. Questionable : it has been mentioned but no negative / positive

evidence 4. Unmentioned : Lack of any kind of evidence / never

mentioned

Considering more features or patterns Advantages : Hope of capturing more evidence to support

“Yes/Exists” Answer. Disadvantages : May lead to the absorption of more noise by

the system and impact the identification of other major terms and concepts, and therefore the overall performance of the system.



The system :We designed a customized system to address the common

challenge of both issues, which is Noise reduction.

Methodology: Using rules, different techniques in language processing

algorithms, a decision tree classifier and some innovative solutions, a system was developed specifically for these types of noise prone corpora.

Idea : We kept the number of features to monitor (for each co-

morbidities) as low as possible. “based on the proposition that concepts are best defined in a few

features and many features would add noise to the classifier.”



729(Training) + 310(Test) Clinical notes Obesity and 15 co-morbidities A Search Concept can be labeled as

Yes/No/Unmentioned/Questionable for obesity and each co-morbidity.

E.g. Search answer for Case #110 : Obesity : Yes Diabetes : No CHF : Unmentioned

Cases have variable sizes between 240 Words to 5000 Words.



Discharge Summaries

1

Negation Analysis

Computing minimal feature

set

Applying high level Classifiers

Adjusting feature set

for dependent Classifiers

Applying dependent Classifiers

3

Applying noise

reduction rules

2

Applying 2nd Round

of noise reduction

Filtering suspected Noisy results using External

Knowledge source

FilteringFilteringmisleadinmisleadin

gg data data sectionssections

Answers to search concepts

4

8Identifying clinical concepts in a noise prone environment



Discharge Date: 6/26/1990Discharge Date: 6/26/1990 HISTORY OF PRESENT ILLNESS: This is a 37 year old female HISTORY OF PRESENT ILLNESS: This is a 37 year old female

who haswho has had pain in her old appendectomyhad pain in her old appendectomy incision. The patient has had pain intermittently in the rightincision. The patient has had pain intermittently in the right lower quadrant in the old appendectomy scar for many years. lower quadrant in the old appendectomy scar for many years.

SheShe denies nausea or vomiting , or history of intestinal obstruction.denies nausea or vomiting , or history of intestinal obstruction. Family History : not obese , no evidence of cancer or CHF. Family History : not obese , no evidence of cancer or CHF.

Diabetes .Diabetes . PAST MEDICAL HISTORY: significant for PAST MEDICAL HISTORY: significant for hypertension? hypertension? . She . She

had an appendectomy in 1965. She had a right carpal tunnel had an appendectomy in 1965. She had a right carpal tunnel release inrelease in

1985 , and a right wrist tendon surgery in 1987. She has 1985 , and a right wrist tendon surgery in 1987. She has chronicchronic

obstructive pulmonary disease. MEDICATIONS ON ADMISSION:obstructive pulmonary disease. MEDICATIONS ON ADMISSION: Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies. ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES

NAUSEA AND VOMITING. She does not smoke and only NAUSEA AND VOMITING. She does not smoke and only occasionally drinks. occasionally drinks.

REVIEW OF SYSTEMS: No evidence for : hypertension , CAD.REVIEW OF SYSTEMS: No evidence for : hypertension , CAD. PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate

is 80.is 80. In general , In general , this is an overweight this is an overweight , otherwise, otherwise were 2+ in the radial and dorsalis pedis. Abdomen: Soft , were 2+ in the radial and dorsalis pedis. Abdomen: Soft ,

obeseobese , , nontender , with some mild incisional tenderness over the nontender , with some mild incisional tenderness over the

area ofarea of the appendectomy scar. Neurological examination was the appendectomy scar. Neurological examination was

nonfocalnonfocal..

Discharge Date: 6/26/1990

HISTORY OF PRESENT ILLNESS: HISTORY OF PRESENT ILLNESS: This is a 37 year old female who has had pain in her old appendectomyThis is a 37 year old female who has had pain in her old appendectomyincision. incision. The patient has had pain intermittently in the right lower quadrant in the old The patient has had pain intermittently in the right lower quadrant in the old appendectomy scar for many years. appendectomy scar for many years. She denies nausea or vomiting , or history of intestinal obstruction.She denies nausea or vomiting , or history of intestinal obstruction.

Family History :Family History : not obese , no evidence of cancer or CHF. Diabetes .not obese , no evidence of cancer or CHF. Diabetes .

PAST MEDICAL HISTORYPAST MEDICAL HISTORY: : significant for hypertension?significant for hypertension? . . She had an appendectomy in 1965. She had a right carpal tunnel release inShe had an appendectomy in 1965. She had a right carpal tunnel release in1985 , and a right wrist tendon surgery in 1987. She has chronic1985 , and a right wrist tendon surgery in 1987. She has chronicobstructive pulmonary disease. obstructive pulmonary disease.

MEDICATIONS ON ADMISSION:MEDICATIONS ON ADMISSION:Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.

ALLERGIES:ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA AND PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA AND VOMITING. She does not smoke and only occasionally drinks. VOMITING. She does not smoke and only occasionally drinks.

REVIEW OF SYSTEMS:REVIEW OF SYSTEMS: No evidence for : hypertension , CAD. No evidence for : hypertension , CAD.

PHYSICAL EXAMINATION: PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate is 80.Blood pressure is 130/90 , heart rate is 80.In general , In general , this is an overweight this is an overweight , otherwise, otherwisewere 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,were 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,nontender , with some mild incisional tenderness over the area ofnontender , with some mild incisional tenderness over the area ofthe appendectomy scar. Neurological examination was nonfocal.the appendectomy scar. Neurological examination was nonfocal.





Family History :Family History : not obese , no evidence of cancer or CHF. Diabetes .not obese , no evidence of cancer or CHF. Diabetes .

PAST MEDICAL HISTORYPAST MEDICAL HISTORY: : significant for hypertension?significant for hypertension? . . She had an appendectomy in 1965. She had a right carpal tunnel release inShe had an appendectomy in 1965. She had a right carpal tunnel release in1985 , and a right wrist tendon surgery in 1987. She has chronic1985 , and a right wrist tendon surgery in 1987. She has chronicobstructive pulmonary disease. obstructive pulmonary disease.







Family History :Family History : not obese , no evidence of cancer or not obese , no evidence of cancer or CHF. Diabetes .CHF. Diabetes .

PAST MEDICAL HISTORYPAST MEDICAL HISTORY: : significant for hypertension? significant for hypertension? . . She had an appendectomy in 1965. She had a right carpal She had an appendectomy in 1965. She had a right carpal tunnel release intunnel release in1985 , and a right wrist tendon surgery in 1987. She had 1985 , and a right wrist tendon surgery in 1987. She had chronicchronicobstructive pulmonary diseaseobstructive pulmonary disease. .








HISTORY OF PRESENT ILLNESS: HISTORY OF PRESENT ILLNESS:

This is a 37 year old female who has had pain in her old This is a 37 year old female who has had pain in her old appendectomyappendectomy

incision. incision.

The patient has had pain intermittently in the right lower quadrant in The patient has had pain intermittently in the right lower quadrant in the old appendectomy scar for many years. the old appendectomy scar for many years.

She denies nausea or vomiting , or history of intestinal obstruction.She denies nausea or vomiting , or history of intestinal obstruction.

MEDICATIONS ON ADMISSION:MEDICATIONS ON ADMISSION:

Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.

ALLERGIES:ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA AND VOMITING. She does not smoke and only occasionally drinks. AND VOMITING. She does not smoke and only occasionally drinks.


PHYSICAL EXAMINATION: PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate is 80.Blood pressure is 130/90 , heart rate is 80.

In general , In general , this is an overweight this is an overweight , otherwise, otherwise

were 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,were 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,

nontender , with some mild incisional tenderness over the area ofnontender , with some mild incisional tenderness over the area of

the appendectomy scar. Neurological examination was nonfocal.the appendectomy scar. Neurological examination was nonfocal.


HISTORY OF PRESENT ILLNESS: HISTORY OF PRESENT ILLNESS:

This is a 37 year old female who has had pain in her old This is a 37 year old female who has had pain in her old appendectomyappendectomy

incision. incision.

The patient has had pain intermittently in the right lower quadrant in The patient has had pain intermittently in the right lower quadrant in the old appendectomy scar for many years. the old appendectomy scar for many years.

She denies nausea or vomiting , or history of intestinal obstruction.She denies nausea or vomiting , or history of intestinal obstruction.

MEDICATIONS ON ADMISSION:MEDICATIONS ON ADMISSION:

Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.Hydrochlorothiazide 25 q-day and Seldane p.r.n. for allergies.

ALLERGIES:ALLERGIES: PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA PENICILLIN CAUSES A RASH , MORPHINE CAUSES NAUSEA AND VOMITING. She does not smoke and only occasionally drinks. AND VOMITING. She does not smoke and only occasionally drinks.

REVIEW OF SYSTEMS:REVIEW OF SYSTEMS: No evidence for No evidence for : : hypertensionhypertension , , CAD.CAD.

PHYSICAL EXAMINATION: PHYSICAL EXAMINATION: Blood pressure is 130/90 , heart rate is 80.Blood pressure is 130/90 , heart rate is 80.

In general , this is an overweight , otherwiseIn general , this is an overweight , otherwise

were 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,were 2+ in the radial and dorsalis pedis. Abdomen: Soft , obese ,

nontender , with some mild incisional tenderness over the area ofnontender , with some mild incisional tenderness over the area of

the appendectomy scar. Neurological examination was nonfocal.the appendectomy scar. Neurological examination was nonfocal.

Co-morbidities

• 1% = 6 cases• F1 Measure

Bag of words & SVM

Info-gain , Customized feature selection , Noise reduction Uni-grams

N-grams, Enhanced negation, Accurate Feature selection & Tree J48

Prefixes , Drug names, disease signs and symptoms. Multi-level classifiers

Obesity 81% 94% 96% 96%

Asthma 82% 96% 98% 98.68%

CAD 77% 89.56% 89.56% 91.10%

CHF 74% 94% 94.2% 95.84%

Depression

82% 96.55% 96.55% 96.55%

DM 79% 92.4% 92.5% 93.4%

GERD 81% 97.1% 98% 98%

Hyper_chol

71% 88.65% 90% 92.2%

HTN 81% 94.7% 94.7% 95%

Hyper_trig 61% 97.37% 97.37% 97.37%

OA 62% 86.4% 87% 91.2%

OSA 80% 98.36% 98.36% 99%



a b c d <-- classified as

246 0 23 0 Yes = a

2 0 5 0 No = b

3 0 342 0 Unmentioned = c

0 0 0 0 Questionable = d

a b c d <-- classified as

265 0 4 0 Yes = a

2 0 5 0 No = b

14 0 331 0 Unmentioned = c

0 0 0 0 Questionable = d

After Step 3: After Step 3: 1.6% Increase Total1.6% Increase Total

82% Decrease in False Negative 82% Decrease in False Negative



1. Search Concepts within noise prone environment has its limitations and requirements.

2. Adding more features to classifiers gives us more accuracy for “Yes/Exist” class and more noise as side effect.

3. Looking for “unmentioned” Concepts is very sensitive to noise.

4. Enhanced Negation identifier increased the accuracy of ‘Yes’ (Positive search results) Class significantly.

5. Introducing prefix-phrases reduced the level of noise significantly in favor of ‘Unmentioned class’

6. Adding DRUG list changed the classification matrix to better classification for ‘Yes’ Class but because of Noise absorbing ‘Unmentioned’ class accuracy decreased.

7. Multi-level classifier , led to less false negative results

14

Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory...

Documents

Transcript of Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory...