NLP for Health Informatics: text-mining patient records

1. School of Computing FACULTY OF ENGINEERING NLP for Health Informatics: text-mining patient records SNOMED CT based semantic tagging of medical narratives Verbal Autopsy corpus for Machine Learning of Cause of Death E-Health GATEway to the Clouds SamanHina, Sammy Danso, Eric Atwell, Owen Johnson Natural Language Processing Group

2. School of Computing FACULTY OF ENGINEERING SNOMED CT based semantic tagging of medical narratives --------------------------------------------------------------------- • Research Objective • Key Challenges • Resources • Methods 1. Baseline Application 2. SNOMED CT Rule-based semantic tagger • Results • Conclusion and Future Work

3. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Sample Text Output

4. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Research Objective --------------------------------------------------------------------- To design a novel approach for extraction of semantic information from unstructured medical narratives. The underlying research hypothesis is that it is possible to annotate natural language medical narratives with high accuracy using SNOMED CT healthcare data standard. Healthcare Data standards • Secure • Consistent • Authentic sharing among healthcare users with codes.

5. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Key Challenges --------------------------------------------------------------------- • Clinicians have different ways of expressing one single medical term and do not follow language of healthcare data standards which is a challenge in extracting domain knowledge. • Not having domain expert. • Use of synonyms, abbreviations , paraphrasing the concepts and different preferred names of a concept increases the complexity of the current research challenge. • Different patterns of section headers, capitalization of words and content.

6. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING

7. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Corpus ----------------------------------------------------------------------- • Corpus from the fourth i2b2/VA 2010 challenge. • Contains discharge summaries and progress notes from four healthcare partners.

8. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Data Standard ------------------------------------------------------------------ SNOMED-CT(Systematized Nomenclature of Medicine Clinical Terms) a comprehensive international data standard for clinical terminology. • Number of Concepts from SNOMED CT : 356,432 • 16 out of 31Semantic types from SNOMED CT have been used to develop SNOMED CT semantic tagger. • Attribute 9. Person • Body Structure 10. Physical Object • Disorder 11. Procedure • Environment 12. Product Or Substance • Findings 13. Qualifier Value • Observable Entity 14. Record Artifact • Occupation 15. Regime/ Therapy • Organism 16. Situation

9. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Annotation scheme for Gold Standard Corpus -------------------------------------------------------------------- • Pre annotation of corpus using SNOMED CT dictionary application (Baseline system). • Reviewing the corpus manually and mark the remaining concepts considering the following language issues; Synonyms, abbreviations, incomplete concepts, paraphrase of concepts and concepts under section headings. • Concepts which are not identified correctly should be removed. • In case of non domain user, NCBO bioportal annotator will be used to annotate the gold standard corpus by searching the key words and bigrams of the possible concepts.

10. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING • Concepts should be marked up to three levels of granularity. • Agreement of gold standard is more than 90 %.

11. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Baseline System - SNOMED CT Dictionary Application ----------------------------------------------------------------------- • Basic language processing (Tokenize, Sentence Splitting, POS tagging) • Concepts have been tagged automatically (Dictionary, Lookup). • SNOMED CT knowledge base was developed by constructing separate dictionaries of 16 semantic types. • 6 out of 16 tags performed well with dictionary application. 1. Disorder 4. Record Artifact 2. Observable Entity 5. Regime/Therapy 3. Person 6. Situation

12. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Optimization of SNOMED CT Knowledgebase --------------------------------------------------------------- • Optimizing the concepts in SNOMED CT semantic types to write general rules for semantic tagger. • Optimization process reduce the size of knowledge base by removing un necessary and ambiguous information. Entire lung -> Lung Ear NOS -> Ear • Long multiword concepts have been transformed into individual concepts to solve paraphrasing problem. Radiography of chest and lung -> 1. Radiography 2. Chest 3.lung

13. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Rule-based SNOMED CT Semantic tagger --------------------------------------------------------------- This application use the optimized SNOMED CT dictionary as knowledgebase. Rules Documents containing narratives Colour coded SNOMED CT Semantic types Extracting concepts and plural concepts Tokenizer Sentence Splitter Part Of Speech Tagger Morphological Analyzer SNOMED CT knowledge base

14. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING

15. PhD Annual Symposium-2011 School of Computing FACULTY OF ENGINEERING Conclusion and Future Work --------------------------------------------------------------- • Corpus containing long multiword concepts has been automatically extracted and tagged with 10 out 16 SNOMED semantic types. • Annotation of unseen test corpus will be completed by domain users to test SNOMED CT semantic tagger. • Optimization of the remaining SNOMED CT semantic types to construct general rules. • Corpus annotations will be contributed to the users through i2b2 organizers.

16. Samuel Danso1,3, Eric Atwell1, Owen Johnson1,  Guus ten Asbroek2,  Seyi Soromekun2, Karen Edmond2, Chris Hurt4, Lisa Hurt2, Charles Zandoh3, Charlotte Tawiah3, Zelee Hill2, Justin Fenty2, SeebaAmenga Etego3, Seth Owusu Agyei2,3, and Betty R Kirkwood2. 1 University of Leeds 2 London School of Hygiene and Tropical Medicine 3 Kintampo Health Research Centre, Ghana 4 University of Cardiff Presented By Samuel Danso PhD Student - NLP Research Group, University of Leeds scsod@leeds.ac.uk 21st July 2011

18. Causes of Death Information – The global picture About 57 million people die each year Cause of Death Information is vitally important to health planners and policy makers at all levels. How do we find out the 67% ? Verbal Autopsy

19. Use of CoD Information Source Byass et al, 2007

20. basically, a narrative of an account of an incident that led to the death of a person. • An idea from the 17th Century used in the UK and other developed countries. Now recommended by WHO as the standard approach used in the developing countries.

23. Sample of VA Data for Infant Death I Coded part

24. Sample of VA Data for Infant Death II free text part

30. Characteristics of corpus

31. Data sparseness and imbalance - 46 categories

32. Characteristics of corpus: free text Some Statistics

33. Characteristics of corpus: free text • Spelling and grammatical mistakes posing parsing problems Misspellings Grammatical error Inappropriate use of punctuation marks “WHEN THE CHILD WAS SIXTEEN (16) DAYS OLD SHE FELL SICK WHICH LAUTED FOR THREE (3) DAYS BEFORE SHE DIED. THE CHILD HAVING DIFFICULT BREATING. ANY TIME, SHE BREATHS, YOU SEE A HOLE IN THE CHEST, AND ALSO MAKING NOISE IN THE CHEST. SHE HAD CONVULSION WHEN SHE WAS SEVERTEEN (17) DAYS OLD BEFORE SHE DIED THE FOLLOWING DAY. SHE ALSO HAD A BULGING FONTENED AND SEVERE HOT BODY WHICH LASTED FOR TWO (2) DAYS BEFORE SHE DIED. THE CHILD ALSO HAD A FIT WHICH SHE COULD NOT OPEN HER MOUTH.”

34. Different ways of expressing the same concept. • Baby came out • Baby landed • Gave birth • Local words • “ • ‘afam’ • ‘bentoa’ • Abbreviations • ANC = Antenatal Clinic • TBA = Traditional Birth Antendant • Fuzzy expression of clinical concepts. Sometimes no clinical concept expressed at all. (..”I visited Kintampo hospital on Tuesday and was given one drip of water. ..”) Delivery

35. Missing values (-) • 215 variables • Entries are coded • sex = 1, 2, 8 or 9 • Weight= 1.45, 9.99 or 8.88 • Continues revision of questionnaire resulting in blank values for some variables

37. Results: 46 categories - combined dataset % Accuracy of correctly classified instances

38. Results: 6 categories – combined dataset

39. Results: 46 categories – time of death

40. Results: 6 categories – time of death

41. Discussion and Conclusion • Key lessons • CRISP-DM is the appropriate methodology for this project • It is feasible to use machine learning techniques to classify CoD in Verbal Autopsies • Split of dataset by clinical definitions into homogenous sets improves classifier performance • Classification at top level of hierarchy of CoD could lead to increase in performance across classifiers due to number of classes (46 to 6) and instances per class.

42. Discussion and Conclusion Other Uses of corpus?

43. e-Health GATEway to the Clouds http://www.comp.leeds.ac.uk/nlp/e-health • WP1: Clouds on the White Rose Grid VRE • Deliverables: A secure cloud-based VRE on the White Rose Grid (Month 2), e-health records from TPP stored (Month 3), access and research support tools (Month 3). Iterative refinement (Month 3-5). • WP2: GATEway component • Deliverables: A GATE plug-in module capable of securely pseudonymising the free text elements of the example e-health records (Month 3). Iterative refinement (Month 3-5). • WP3: Evaluation and Sustainability • Deliverables: Evaluation of WP1 and WP2 combined into a cohesive e-health VRE (Month 5), sustainability plan (Month 4), dissemination as a case study (mid Month 5), hand-over to ongoing support by YCHI (Month 6)

44. We welcome e-Health MSc / PhD Projects School of Computing FACULTY OF ENGINEERING SNOMED CT based semantic tagging of medical narratives Verbal Autopsy corpus for Machine Learning of Cause of Death E-Health GATEway to the Clouds SamanHina, Sammy Danso, Eric Atwell, Owen Johnson Natural Language Processing Group