Identifying concepts in a noise prone environment: Looking up Obesity and its 15 co-morbidities In patient discharge summaries

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Identifying 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
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Overview

• 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.

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SAMPLE 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.

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1st 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.

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2nd 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.

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Goal 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.

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Data 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.

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Discharge 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
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SAMPLE 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.

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SAMPLE 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.

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SAMPLE 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 ,

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After Step 3 Less False negtive
After Step 3 1.6 Increase Total 82
Decrease in False Negative
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Summary

• 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