Tapping into the Potential of Natural Language Processing in Healthcare
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Gathering insight from clinical notes remains one of the areas of untapped healthcare intelligence with tremendous potential. But extracting that value is difficult. Still, a few organizations across the country are demonstrating success using advanced technology tied to intuitive processes and procedures. Leading one such organizational effort is Wendy Chapman, PhD, chair of the Department of Biomedical Informatics at the University of Utah. Dr. Chapman’s research has driven discovery in new ways to disseminate resources for modeling and understanding information described in narrative clinical reports. Her teams have demonstrated phenotyping for precision medicine, quality improvement, and decision support. Joining Dr. Chapman in a shared discussion is Mike Dow who leads the Natural Language Processing (NLP) technology team at Health Catalyst. Mike and team have several years of experience engaging with a variety of health system organizations across the country who are realizing statistical insight by incorporating text notes along with discrete data analysis. Together, Mike and Dr. Chapman will provide an NLP primer sharing principle-driven stories so you can get going with NLP whether you are just beginning or considering processes, tools or how to build support with key leadership. Learning Objectives: - Understand NLP, both its challenges, and potential to drive clinical insight using social determinants of health - Gain insight into the technology that makes NLP possible - Consider the future potential of NLP View this webin to better understand the potential of NLP through existing applications, the challenges of making NLP a real and scalable solution, and walk away with concrete actions you can take to use NLP for the good of your organization.
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Tapping into the Potential of Natural Language Processing in Healthcare
- 1. Tapping Into the Potential of Natural Language Processing in Healthcare Wendy Chapman, PhD Chair, Department of Biomedical Informatics, University of Utah School of Medicine Mike Dow Senior Director, Product Development, Health Catalyst
- 2. Act 1 The Possibilities are Endless
- 3. © 2018 Health Catalyst Healthcare Spending Per Capita vs. Average Life Expectancy Among OECD Countries 3
- 4. © 2018 Health Catalyst 4 The US Health Care System is in Crisis That means the US Economy is in Crisis
- 5. © 2018 Health Catalyst Crisis as an Opportunity 5 Big Data Learning Health System
- 7. © 2018 Health Catalyst Adoption of Electronic Health Records 7
- 8. © 2018 Health Catalyst Your Electronic Health Record? 8 https://www.youtube.com/watch?v=VHMJaV7zJxE#t=242
- 11. © 2018 Health Catalyst 50% of Patient Time Spent on EHR 11
- 12. The Possibilities Pain is Endless
- 13. Act 2 NLP to the Rescue (aka “The Hype”)
- 16. © 2018 Health Catalyst Natural Language Processing 16 Natural Language Processing Structured Data (Machine Interpretable) MEDLINE Articles / Abstracts Electronic Medical Records • Classify • Extract • Summarize
- 17. © 2018 Health Catalyst Poll Question #1 Are you currently using NLP in your work? 1. Yes — 33% 2. No — 67% 17
- 20. © 2018 Health Catalyst Harvest – New York Presbyterian 20 • Scalable, distributed NLP • Problem salience computation • Presentation of information from multiple care settings Noemie Elhadad JAMIA, 2014 http://jamia.oxfordjournals.org/content/early/2014/11/07/amiajnl-2014-002945
- 22. © 2018 Health Catalyst 22 “Made me more confident that I wasn’t missing information that can sometimes be buried in the list of [past medical history].” “It helped pick up on diagnoses within the chart that I otherwise would’ve had a lot of difficulty finding.”
- 24. © 2018 Health Catalyst Predictive Analytics 24 Image: Getty Image: Vicky Leta / Mashable
- 25. © 2018 Health Catalyst Exploratory Analysis of Social Media Prior to a Suicide Attempt 25 Glen Coppersmith Qntfy glen@qntfy.com Kim Ngo Qntfy, University of Notre Dame kim@qntfy.com Ryan Leary Qntfy ryan@qntfy.com Anthony Wood Qntfy tony@qntfy.com 2014 suicide rate in US was 13 per 100,000 people • 24% increase in last decade Predict 70% of suicide attempts • 10% false positive rate http://www.aclweb.org/anthology/W16-0311
- 26. © 2018 Health Catalyst 26 Fewer emojis • Narrow group More tweets with sadness • Increase in angry and sad tweets before attempt Number of Emojis in Tweets No Attempt Before Attempt After Attempt
- 28. © 2018 Health Catalyst Phenotyping 28 Physical appearance Biochemical processes Behavior Phenotype The observable physical or biochemical expression of a specific trait in an organism
- 30. © 2018 Health Catalyst Natural Language Processing 30 Severe Carotid Stenosis VA Patients Treatment Yes No Exclude CompareMedication Surgery NLP Salomeh Keyhani, Wendy Chapman, Danielle Mowery Salomeh Keyhani
- 31. © 2018 Health Catalyst Deep Computable Phenotyping 31 Yes Correlate Cancer Genome Investigation Phenotypes No Need to be able to identify richer phenotypes Guergana SavovaHarry HochheiserRebecca Jacobson
- 32. © 2018 Health Catalyst Natural Language Processing 32 Breast Cancer: Yes/No Slide courtesy of Harry Hochheiser
- 33. © 2018 Health Catalyst Answer Questions Like… 33 What histologic types of breast cancer are associated with patients that have a substitution mutation on BRCA-1? For patients with a papillary breast carcinoma that underwent neoadjuvant treatments regimen, what number of patients have had a recurrence or metastasis?
- 35. © 2018 Health Catalyst 35 Andrew Gawron, SLC VA Adenoma detection rate (ADR) Colonoscopies with 1 adenoma All screening colonoscopies
- 36. © 2018 Health Catalyst 36 Chart Review or NLP ADR Colonoscopy and Pathology Reports Andrew Gawron
- 37. © 2018 Health Catalyst 37 1% in ADR 3% in Cancer Mortality
- 38. Act 3 A Peek Under the Hood (aka “The Reality”)
- 41. © 2018 Health Catalyst The Challenges Why isn’t NLP Completely Pervasive? 41
- 42. © 2018 Health Catalyst Garbage in, Garbage Out Shortcuts for documentation 42 Cardiovascular: [ ] Angina [ ] MI [x ] HTN [ ] CHF [ ] PVD [ ] DVT [ ] Arrhythmias [ ] Previous PTCA [ ] Previous Cardiac Surgery [ ] Negative - Denies CV problems Templates
- 46. © 2018 Health Catalyst 46 58 Classes of Formats Dezon Finch http://scholarcommons.usf.edu/cgi/viewcontent.cgi?article=5517&context=etd
- 47. © 2018 Health Catalyst Garbage in, Garbage Out Shortcuts for documentation 47 Copy & Paste • Note • Outdated or inaccurate • No author • Propagation of false information
- 48. © 2018 Health Catalyst The Challenges Why isn’t NLP Completely Pervasive? 48
- 49. © 2018 Health Catalyst Knowledge Representation 49 Phenotype: Cough • At least two episodes of severe cough in one year
- 50. © 2018 Health Catalyst Phenotype Variables in Layers 50 At least two episodes of severe cough in one year
- 51. © 2018 Health Catalyst Instance: Map Cough to UMLS 51
- 52. © 2018 Health Catalyst 3 day hx of hacking cough. How long does the cough need to land to meet your criteria? Do changes over time matter? 52 The cough has worsened over the last 24 hours. The patient was given medication X and the cough subsided. However, an hour after administration the severe cough returned. What about response to treatment? Does severity matter?
- 53. © 2018 Health Catalyst 53 Why isn’t NLP Completely Pervasive? The Challenges
- 54. © 2018 Health Catalyst Sublanguage 54 Zellig Harris • Sublanguage is a subset of natural language 1. Uses a subset of vocabulary and grammatical rules 2. Regularity and peculiarities • Semantic • Syntactic
- 55. © 2018 Health Catalyst Social Media Sublanguage 55 Altered Vocabulary: Status, update New Vocabulary: Selfie Emoticons: Abbreviations: TTOL, LOL, ROTFL Hashtags: #jointpain Punctuation: .
- 56. © 2018 Health Catalyst Medical Sublanguage 56 Medical Blog Clinical Notes Broad Use of Verbs Limited Use of Verbs Measurements General Clinical Descriptions Fewer Semantic Types Broader Semantic Types
- 57. © 2018 Health Catalyst 57 Why isn’t NLP Completely Pervasive? The Challenges
- 58. © 2018 Health Catalyst Variations on Variations Different Words with the Same Meaning Linguistic Variation 58 Derivation • Mediastinal = Mediastinum Inflection • Opacity = Opacities; Cough = Coughed Synonym • Addison’s Disease: Addison melanoderma, adrenal insufficiency, adrenocortical insufficiency, asthenia pigmentosa, bronzed disease, melasma addisonii … • Chest Wall Tenderness: Chest wall did demonstrate some slight tenderness when the patient had pressure applied to the right side of the thoracic cage
- 59. © 2018 Health Catalyst Polysemy One Word with Multiple Meanings 59 General polysemy • Patient was prescribed codeine upon discharge • The discharge was yellow and purulent Acronyms and Abbreviations • APC: activated protein c, adenomatosis polyposis coli, adenomatous polyposis coli, antigen presenting cell, aerobic plate count, advanced pancreatic caner, age period cohort, alfalfa protein concentrated, allophycocyanin, anaphase promoting complex, anoxic preconditioning, anterior piriform cortex, antibody producing cells, atrial premature complex …
- 60. Act 4 You Can Do It!
- 61. © 2018 Health Catalyst 61 High Hanging Fruit Low Hanging Fruit
- 62. © 2018 Health Catalyst Low Hanging Fruit 62 Explicit Mentions • “Patient denies chest pain” = Chest_pain – negated
- 63. © 2018 Health Catalyst Low Hanging Fruit 63 Explicit Mentions • “Patient denies chest pain” = Chest_pain – negated Expected Classes & Relations • Diseases • Problems • Anatomic locations
- 64. © 2018 Health Catalyst Low Hanging Fruit 64 Explicit Mentions • “Patient denies chest pain” = Chest_pain – negated Expected Classes & Relations • Diseases • Problems • Anatomic locations Unambiguous Vocabulary • Pneumonia • Lobe • Stenosis • Severe
- 66. © 2018 Health Catalyst Poll Question #2 If you are currently using NLP, what are you using if for? 1. Quality — 16% 2. Research — 23% 3. Decision support — 18% 4. Predictive analytics — 27% 5. Other — 16% 66
- 68. © 2018 Health Catalyst Quality Pilot Deployment Across the U.S. in the VA 68
- 70. © 2018 Health Catalyst Research 70 Severe Carotid Stenosis Treatment Yes No Exclude CompareMedication Surgery NLP Salomeh Keyhani, Wendy Chapman, Danielle Mowery Decreased chart review by 70%
- 75. © 2018 Health Catalyst 75 High Hanging Fruit Low Hanging Fruit
- 76. © 2018 Health Catalyst High Hanging Fruit 76 Requires Inference • “Brother at bedside” = Has_Social_Support
- 77. © 2018 Health Catalyst High Hanging Fruit 77 Requires Inference • “Brother at bedside” = Has_Social_Support Ambiguous Vocabulary • “Brother died from MI” • “Stood at bedside”
- 78. © 2018 Health Catalyst High Hanging Fruit 78 Requires Inference • “Brother at bedside” = Has_Social_Support Ambiguous Vocabulary • “Brother died from MI” • “Stood at bedside” Semantic Roles Matter • “Wife helps patient with meds” • “Patient helps wife with meds”
- 79. © 2018 Health Catalyst Example 79 Social Risk Factors to help predict readmission
- 80. © 2018 Health Catalyst Using NLP to Extract High Fruit 80 Dementia Depression Activities of Daily Living • Bath, Eat, Walk Social Support Housing Situation Language Barrier Medical Condition Leading to Impairment Medication Compliance F-score 75-98%
- 81. Conclusion
- 82. © 2018 Health Catalyst By the way… 82 Amazon just released a clinical NLP tool • Get a feel for what clinical NLP tools do Many other tools • Contextual information • Classification
- 83. © 2018 Health Catalyst Opportunities Abound for Using NLP in Health Care 83 1. Identify information from text • Many tools available • A lot of low hanging fruit 2. Create apps using NLP output 3. Integrate into workflow Find a partner – Health Catalyst
- 85. Q&A
- 86. © 2018 Health Catalyst Over 100 years ago, healing professionals and healthcare itself went through a massive transformation that led us to the models of care delivery that we use today. Dr. Brent James argues that we are now, again, at a once-in-a-century inflection point to change the course of healthcare. Change takes real effort, but provides massive opportunity. Wednesday, December 19 1:00-2:00 PM EST Learn how to: • Use data to find variations in both cost and quality of care. • Standardize care without demotivating underperforming outliers. • Build a culture of data-driven care providers. • Develop an improvement strategy that you can start today. Why Clinical Quality Should Be Your Core Business Strategy 86 BRENT C. JAMES, MD MStat, and Former Vice President and Chief Quality Officer, Intermountain Healthcare Wendy Chapman earned her bachelor’s degree in Linguistics and her PhD in Medical Informatics Brent James is known internationally for his work in clinical quality improvement, patient safety, and the infrastructure that underlies successful improvement efforts, such as culture change, data systems, payment methods, and management roles.
- 87. Thank You!