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Update README.rst
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Changed 'cliner predict' to 'python cliner predict' 
Changed 'cliner evaluate' to 'python cliner evaluate'
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shuvoxcd01 authored Jul 21, 2020
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Expand Up @@ -82,15 +82,15 @@ This example trains a very simple CliNER model. The (pretend.txt, pretend.con) p

Once your CliNER model is built, you can use it to predict concepts in text files.

cliner predict --txt data/examples/ex_doc.txt --out data/test_predictions/ --format i2b2 --model models/foo.model
python cliner predict --txt data/examples/ex_doc.txt --out data/test_predictions/ --format i2b2 --model models/foo.model

In this example, we use the models/foo.model CliNER model that we built up above. This model is used to predict concepts in i2b2 format for the "ex_doc.txt" file. This generates a file named "ex_doc.con" and stores it in the specified output directory.

(4) Evaluation

This allows us to evaluate how well CliNER does by comparing it against a gold standard.

cliner evaluate --txt data/examples/ex_doc.txt --gold examples --predictions data/test_predictions/ --format i2b2
python cliner evaluate --txt data/examples/ex_doc.txt --gold examples --predictions data/test_predictions/ --format i2b2

Evaluate how well the system predictions did. Both sets of data must be in the same format, and that format must be specified. This means that both the examples and data/test_predictions directories contain the file pretend.con.

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