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Selection of Clinical Trials: Knowledge Representation and Acquisition

Selection of Clinical Trials: Knowledge Representation and Acquisition. Savvas Nikiforou. Committee: Eugene Fink Lawrence O. Hall Dmitry B. Goldgof. Part of the project:. Automated Matching of Patients to Clinical Trials. Faculty: Lawrence O. Hall Dmitry B. Goldgof Eugene Fink.

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Selection of Clinical Trials: Knowledge Representation and Acquisition

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  1. Selection of Clinical Trials:Knowledge Representation and Acquisition Savvas Nikiforou Committee: Eugene Fink Lawrence O. Hall Dmitry B. Goldgof

  2. Part of the project: Automated Matching of Patients to Clinical Trials Faculty: Lawrence O. Hall Dmitry B. Goldgof Eugene Fink Students: Lynn Fletcher Princeton Kokku Savvas Nikiforou Bhavesh Goswami Tim Ivanovskiy Rebecca Smith

  3. Expert System The system analyzes a patient’s data and determines whether the patient is eligible for Moffitt clinical trials.

  4. Expert System • Guides a clinician through related questions • Identifies appropriate medical tests • Selects matching clinical trials • Minimizes pain and cost of selection process

  5. Outline • Previous work • Eligibility decisions • Knowledge base • Knowledge entry • Experiments

  6. Previous Work • Medical expert systems • Knowledge acquisition • Medical systems at USF

  7. Medical Expert Systems • If-then rules: • Mycin (1972), Puff (1977), Centaur (1977) • Qualitative reasoning: • Oncocin (1981), Eon (1995), OncoDoc (1998) • Bayesian networks: • Hepar (1990), AIDS2 (1990)

  8. Knowledge Acquisition • Teiresias(1974): Knowledge for Mycin • Salt (1985): Elevator-design rules • Opal (1987): Knowledge for Oncocin • Protégé (1987, 2000):General-purpose tools for developingknowledge acquisition interfaces

  9. Medical Systems at USF Selection of clinical trials for cancer patients • Bayesian networks (Theocharous) • Qualitative reasoning (Fletcher and Hall) No knowledge acquisition tools

  10. Outline • Previous work • Eligibility decisions • Knowledge base • Knowledge entry • Experiments

  11. Example: Eligibility Criteria • Female, older than 30 • No prior surgery • Breast cancer, stage II or III

  12. Example: Questions Female Male Sex: Age: 25

  13. Example: Conclusion Patient is not eligible

  14. Example: Questions Female Male Sex: Age: 35

  15. Example: Questions I II III IV Cancer stage: Prior surgery? Yes No Unknown

  16. Example: Conclusion Patient is eligible

  17. Full Functionality • Orders and groups the questions • Considers multiple clinical trials

  18. Old System • A programmer has to code the questions

  19. New System • A programmer has to code the questions • A nurse enters the questions • through a friendly interface • Problem: Build the interface

  20. Outline • Previous work • Eligibilitydecisions • Knowledge base • Knowledge entry • Experiments

  21. Main Objects • Questions • Medical tests • Eligibility criteria

  22. Types of Questions • Yes / No / Unknown • Multiple choice • Numeric

  23. Cancer stage: I II III IV Age: Examples of Questions Prior surgery? Yes No Unknown

  24. It involves certain pain and cost. Tests A medical test answers several questions.

  25. Example Test: Name and Cost Test name: Mammogram Cost: 50.00 Pain: 1

  26. Example Test: Questions • Yes / No Question: Breast cancer?

  27. I II III IV Example Test: Questions • Multiple choice Question: Options: Cancer stage

  28. Example Test: Questions • Numeric Question: Min Max Prec Tumor size 0 0 25

  29. Eligibility Criteria • A logical expression that determines eligibility for a specific clinical trial

  30. Example: Criteria AND Age > 30 Prior-surgery = NO OR Cancer-stage = II Cancer-stage = III

  31. Outline • Previous work • Eligibilitydecisions • Knowledge base • Knowledge entry • Experiments

  32. Tests and Questions Adding tests Modifying a test Adding yes/no questions Adding multiple choice questions Adding numeric questions Deleting questions

  33. Adding Tests Adding Modifying Yes/No M-Choice Numeric Deleting Test name: Mammography test Cost: 45.50 Pain: 1

  34. Modifying a Test Adding Modifying Yes/No M-Choice Numeric Deleting Test name: Mammography test Mammogram Cost: 45.50 50.00 Pain: 1

  35. Adding Yes/No Questions Adding Modifying Yes/No M-Choice Numeric Deleting • Text Breast cancer?

  36. Adding Multiple Choice Questions Adding Modifying Yes/No M-Choice Numeric Deleting • Text Options Cancer stage I II III IV

  37. Adding Numeric Questions Adding Modifying Yes/No M-Choice Numeric Deleting • Text Min Max Prec Tumor size 0 25 0

  38. Deleting Questions Adding Modifying Yes/No M-Choice Numeric Deleting Breast cancer? Cancer stage Tumor size Patient’s age

  39. Deleting Questions Adding Modifying Yes/No M-Choice Numeric Delete Cancer stage Tumor size

  40. Demo

  41. Selecting questions Defining an expression Deleting expressions Editing questions Eligibility Criteria Selecting tests Adding eligibility criteria

  42. Example: Eligibility Criteria • Female, older than 30 • Breast cancer, stage II • Post-menopausal or surgically sterilized

  43. Adding criteria Selecting tests Adding Eligibility Criteria Selecting questions Defining an expression Deleting expressions Editing questions Trial number Trial name 001 Clinical trial A

  44. Selecting questions Defining an expression Deleting expressions Editing questions Adding criteria Selecting tests Selecting Tests General questions Blood test Mammogram Biopsy Urine test

  45. Adding criteria Selecting tests Selecting Questions Selecting questions Defining an expression Deleting expressions Editing questions Age: From: To: 150 0 30 Cancer stage: I II III IV Prior surgery? Yes No Unknown Post-menopausal? Yes No Unknown Surgically sterilized? Yes No Unknown

  46. Adding criteria Selecting tests Defining an Expression Selecting questions Defining an expression Deleting expressions Editing questions Age > 30 Cancer-stage = II Post-menopausal = YES Surgically-sterilized = YES

  47. Age > 30 Adding criteria Selecting tests Defining an Expression Selecting questions Defining an expression Deleting expressions Editing questions AND Cancer-stage = II Post-menopausal = YES Surgically-sterilized = YES

  48. Age > 30 Cancer-stage = II Adding criteria Selecting tests Defining an Expression Selecting questions Defining an expression Deleting expressions Editing questions AND Post-menopausal = YES Surgically-sterilized = YES

  49. Age > 30 Cancer-stage = II OR Post-menopausal = YES Adding criteria Selecting tests Defining an Expression Selecting questions Defining an expression Deleting expressions Editing questions AND Surgically-sterilized = YES

  50. Age > 30 Cancer-stage = II OR Post-menopausal = YES Surgically-sterilized = YES Adding criteria Selecting tests Defining an Expression Selecting questions Defining an expression Deleting expressions Editing questions AND

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