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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: The fast dictionary pipeline vs. the regular one
Date Sun, 21 Jun 2015 18:45:54 GMT
Sean wrote the fast version and may be able to answer your specific questions. But in general,
the fast dictionary does not match performance exactly -- it is not implementing an equivalent
search and it has different indexing methods. We are happy to receive reports of what seem
like bugs, though, any new software is likely to have some. What I will say is that I know
Sean has run some (as yet unpublished) experiments and we believe that in the aggregate the
new system output is at least as high quality as the older one.

From: Oranit Dror [oranit@algotec.co.il]
Sent: Sunday, June 21, 2015 4:37 AM
To: dev@ctakes.apache.org
Subject: The fast dictionary pipeline vs. the regular one


I am using ctakes 3.2.2 with the regular pipeline. Recently, I have tested the fast dictionary
pipeline and indeed it is much faster.
However, I have encountered with several quality differences in the returned annotations.
For example:

1.       With the fast pipeline, the term "GBM" is annotated as "glioblastoma multiforme",
while in the regular pipeline it is annotated as "glioblastoma".
Note that according to the UMLS DB, the concept of "GBM" is "glioblastoma" and "glioblastoma
multiforme" is mapped to a narrower concept.

2.       The word "cm" in a phrase like "5.5 cm X 2.6 cm" is annotated by the regular pipeline
as "Cutaneous Mastocytosis", while in the fast pipeline it is  not annotated as a medical
term (as expected and as in UMLS).

Any explanation for the differences?

Thank you,

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