What are the tips and tricks for effective use of MedCAT

MedCAT
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What should I look out for when I’m using MedCAT:

  • What is the algorithm good at and not so good at?
  • What should I not use it for?
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Hi @tomolopolis, great questions.

What is the algorithm good at and not so good at (What should I not use it for)?

  • If you need to extract concepts from an existing biomedical ontology (e.g. SNOMED/UMLS) or have your own biomedical ontology, then MedCAT is the tool for you. And if next to this you want to extract contextual annotation for concepts (Negation, Experiencer, …) then you have a standard MedCAT use-case.
  • If you do not have an ontology and are interested in extracting mentions of just one disorder while having a large number of manually annotated documents (i.e. training data) - I’d suggest you go for a standard BERT like approach as it will most likely perform better.

Ended up combining the two questions as they seemed very related, if something is not clear let me know.