Epigenetic states and outcome

Professor Tianxi Cai led a discussion on the study designs to relate epigenetic endopathotypes and clinical outcomes.

Annotation of clinical notes

Guergana led a discussion of the user interface challenges of term selection (in an annotation of a clinical document task). She re-introduced the crew to the UMLS and Concept Unique Identifiers (CUIs). Understanding the dependencies, as Shawn Murphy pointed out is critical to providing users just the right set of terms to pick from (too many terms includes too many irrelevant terms and distracts/consumes the user and too few terms cripples expressivity). So we recognize that knowledge of the UMLS and the medical task is going to be required to optimally select the right set of CUI's to identify patients of interest. Sheng Yu demonstrated work in collaboration with Tianxi Cai that is quite striking in its ability to use the patient corpus to select (rank highly in a pick list) the CUI's of greatest relevance.

NLP games

Cai, Savova et al.

Discussed tradeoffs between performing string matching (hard to scale to the general case, but quite adequate accuracy for well specified and specific narrow cases) and general NLP. Also discussed how to enrich prior probability for a disease of interest to increase performance of high specificity NLP.