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Synonym Test on Precision and Recall
Synonym tables have been grown since the new enhanced system was implemented in 2017 to generate synonyms. This page details a test model for the new enahcned synonyms.
I. Test Data
The terms in the UMLS CORE (Clinical Observations Recording and Encoding) problem list of SNOMED CT are used. They are controlled terminologies to encode clinical information at a summary level, such as the problem list, discharge diagnosis, or reason for encounter secton of an EHR. They are from 8 large scale healthcare insitutions:
References:
Data details:
II. Testing Model
SMT (Synonym Mapping Tools) in STMT package are used to test the performance of synonym.2017. This tool allows users to easily configure different synonym list for subterm sustitution and found the mapped CUI through the expanded terms. The scripts of prgrams are at ${PROJECTS}/STMT/stmt2015/bin/
. Several configurations are set up as follows:
Program | Synonym | UMLS | LVG |
---|---|---|---|
lexSyn.2016 | lexSynonym.2016 | 2016AB | 2016 |
lexSyn.2017 | lexSynonym.2017 | 2016AB | 2016 |
STMT | default synonyms | 2016AB | 2016 |
STMT + lexSyn.2016 (smt.2016AB) | default synonyms + lexSynonym.2016 | 2016AB | 2016 |
STMT + lexSyn.2017 (smt.2017) | default synonyms + lexSynonym.2017 | 2016AB | 2016 |
Model details:
shell> 1.UmlsCore.stmt2015 < ./Inputs/in.stmt2015.lexSyn.2016
shell> 1.UmlsCore.stmt2015 < ./Inputs/in.stmt2015.lexSyn.2017
shell> 1.UmlsCore.stmt2015 < ./Inputs/in.stmt2015.2016AB
shell> 1.UmlsCore.stmt2015 < ./Inputs/in.stmt2015.2017
shell> 2.GetPRFAmia2017
out.LexSynonym.2016AB
0
(Apply SNOMED CT fitler, only work on subNo != 0, Query Expansion)
III. Test Results
Configuration | N. Size | T.P. | F.P. | F.N. | Retrieved | Relevant | Precision | Recall | F1 | Run Time |
---|---|---|---|---|---|---|---|---|---|---|
lexSyn.2016 | 5,070 | 9 | 12 | 2,747 | 21 | 2756 | 42.86% | 0.33% | 0.0065 | 0:16 |
lexSyn.2017 | 149,912 | 287 | 117 | 2,469 | 404 | 2756 | 71.04% | 10.41% | 0.1816 | 3:19 |
STMT | 7,873 | 690 | 353 | 2,066 | 1,049 | 1,402 | 66.16% | 25.04% | 0.3633 | 7:57 |
STMT + lexSyn.2016 | 12,681 | 691 | 358 | 2,065 | 1,049 | 2,756 | 65.87% | 25.07% | 0.3632 | 5:31 |
STMT + lexSyn.2017 | 151,913 | 828 | 424 | 1,928 | 1,252 | 2,756 | 66.13% | 30.04% | 0.4132 | 9:18 |
IV. Discussion
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