Title: Identifying concepts in a noise prone environment: Looking up Obesity and its 15 co-morbidities In patient discharge summaries
1Identifying concepts in a noise prone
environment Looking up Obesity and its 15
co-morbidities In patient discharge summaries
Pooyan Asgari University of Sydney , School of
IT Health Information Technologies Research
Laboratory Supervisor Professor Jon Patrick
2Overview
- 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.
3SAMPLE 51 Obesity ? YESDIABETES Unmentioned
HTN ? NO
HOSPITAL COURSE The patient was taken to the
operating room on 8/6/90 . The procedure
performed was an incisional 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 slow to mobilize. She has
complained of some nausea and some pain in the
abdomen. She was given a PCA pump for the pain.
The patient She 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
her medications. FOLLOWUP She is to be followed
in the office by Dr. Serles as an outpatient.
- 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 of
cancer or CHF. 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.
41st Issue
- 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.
52nd Issue
- 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.
6Goal Noise reduction
- 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. -
7Data Overview
- 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.
8Discharge Summaries
Answers to search concepts
1
Negation Analysis
Filtering suspected Noisy results using External
Knowledge source
Filtering misleading data sections
2
4
Computing minimal feature set
Applying noise reduction rules
Applying dependent Classifiers
3
Applying high level Classifiers
Adjusting feature set for dependent Classifiers
Applying 2nd Round of noise reduction
9SAMPLE 51 Obesity ? YESDIABETES Unmentioned
HTN ? NO
- 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 of
cancer or CHF. 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.
- 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 of
cancer or CHF. 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.
10SAMPLE 51 Obesity ? YESDIABETES Unmentioned
HTN ? NO
- 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 of
cancer or CHF. 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.
- 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 of
cancer or CHF. 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 had 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.
11SAMPLE 51 Obesity ? YESDIABETES Unmentioned
HTN ? NO
- 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. - 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 ,
- 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. - 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 ,
12(No Transcript)
13After Step 3 Less False negtive
After Step 3 1.6 Increase Total 82
Decrease in False Negative
14Summary
- Search Concepts within noise prone environment
has its limitations and requirements. - Adding more features to classifiers gives us more
accuracy for Yes/Exist class and more noise as
side effect. - Looking for unmentioned Concepts is very
sensitive to noise. - Enhanced Negation identifier increased the
accuracy of Yes (Positive search results) Class
significantly. - Introducing prefix-phrases reduced the level of
noise significantly in favor of Unmentioned
class - Adding DRUG list changed the classification
matrix to better classification for Yes Class
but because of Noise absorbing Unmentioned
class accuracy decreased. - Multi-level classifier , led to less false
negative results