Presentation is loading. Please wait.

Presentation is loading. Please wait.

Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory Supervisor : Professor Jon Patrick.

Similar presentations


Presentation on theme: "Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory Supervisor : Professor Jon Patrick."— Presentation transcript:

1 Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory Supervisor : Professor Jon Patrick

2  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

3  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 CHFDiabetes.  Family History : not obese, no evidence of cancer or CHF. Diabetes.  PAST MEDICAL HISTORY : significant for hypertension?. She had an appendectomy in She had a right carpal tunnel release in  1985, and a right wrist tendon surgery in 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 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. 3 Identifying clinical concepts in a noise prone environment

4  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. 4 Identifying clinical concepts in a noise prone environment

5  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. 5 Identifying clinical concepts in a noise prone environment

6 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.” 6 Identifying clinical concepts in a noise prone environment

7  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. 7 Identifying clinical concepts in a noise prone environment

8 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 sourceFiltering misleading data sections Answers to search concepts 4 8 Identifying clinical concepts in a noise prone environment

9 9  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 She had a right carpal tunnel release in  1985, and a right wrist tendon surgery in 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 She had a right carpal tunnel release in 1985, and a right wrist tendon surgery in 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.

10 10 Identifying clinical concepts in a noise prone environment  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 She had a right carpal tunnel release in 1985, and a right wrist tendon surgery in 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 She had a right carpal tunnel release in 1985, and a right wrist tendon surgery in 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.  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.

11 11 Identifying clinical concepts in a noise prone environment  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, 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.  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.

12 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 Obesity81%94%96% Asthma82%96%98%98.68% CAD77%89.56% 91.10% CHF74%94%94.2%95.84% Depression82%96.55% DM79%92.4%92.5%93.4% GERD81%97.1%98% Hyper_chol71%88.65%90%92.2% HTN81%94.7% 95% Hyper_trig61%97.37% OA62%86.4%87%91.2% OSA80%98.36% 99% 12 Identifying clinical concepts in a noise prone environment

13 abcd<-- classified as Yes = a 2050No = b Unmentioned = c 0000Questionable = d abcd<-- classified as Yes = a 2050No = b Unmentioned = c 0000Questionable = d After Step 3: 1.6% Increase Total 1.6% Increase Total 82% Decrease in False Negative After Step 3: 1.6% Increase Total 1.6% Increase Total 82% Decrease in False Negative 13 Identifying clinical concepts in a noise prone environment

14 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


Download ppt "Pooyan Asgari University of Sydney, School of IT Health Information Technologies Research Laboratory Supervisor : Professor Jon Patrick."

Similar presentations


Ads by Google