This script is distributed as apart of the Medical Document Anonymization (MEDDOCAN) task. It is based on the evaluation script from the i2b2 2014 Cardiac Risk and Personal Health-care Information (PHI) tasks. It is intended to be used via command line:
$> python evaluate.py [i2b2|brat] [ner|spans] GOLD SYSTEM
It produces Precision, Recall and F1 (P/R/F1) and leak score measures for the NER subtrack and P/R/F1 for the SPAN subtrack. The latter includes an additional metric where the spans are merged if only non-alphanumerical characters are found between them.
SYSTEM and GOLD may be individual files or also directories in which case all files in SYSTEM will be compared to files the GOLD directory based on their file names.
This software requires to have Python 3 installed on your system.
annotated_corpora/ This directory contains files with annotations Brat annotation format. It may contain different sub-directories for different annotation levels: tokens, sentence splitting, part-of-speech taggin, etc. The sub-directory `sentence_splitting` is mandatory to compute the `leak score` evaluation metric. These files must be stored with `.ann` suffix. gold/ This directory contains the gold standard files in `brat` and `i2b2` format. Each sub-directory may contain different sub-directories for each data set: sample, train, development, test, etc. Files in the latter directories must be in the appropriate format: `.ann` and `.txt` for `brat`, and `.xml` for `i2b2`. system/ This directory contains the submission files in `brat` and `i2b2` format. Each sub-directory may contain different sub-directories for each data set: sample, train, development, test, etc. Each of the previous directories may contain any number of folders, one for each system run. Files in the latter directories must be in the appropriate format: `.ann` and `.txt` for `brat`, and `.xml` for `i2b2`.
It is possible to configure the behavior of this software using the different options.
-
The
i2b2andbratoptions allow to select the input format of the files. -
The
nerandspansoptions allow to select the sub-track. -
The
gs_dirandsys_diroptions allow to select folders. -
Verboseoption allow to control the verbosity level.
The user can select the different options using the command line:
usage: evaluate.py [-h] [-v]
{i2b2,brat} {ner,spans} gs_dir sys_dir [sys_dir ...]
Evaluation script for the MEDDOCAN track.
positional arguments:
{i2b2,brat} Format
{ner,spans} Subtrack
gs_dir Directory to load GS from
sys_dir Directories with system outputs (one or more)
optional arguments:
-h, --help show this help message and exit
-v, --verbose List also scores for each document
Basic Examples:
Evaluate the single system output file '01.xml' against the gold standard file '01.xml' NER subtrack. Input files in i2b2 format:
$> python evaluate.py i2b2 ner gold/01.xml system/run1/01.xml
Report (SYSTEM: run1):
------------------------------------------------------------
Document ID Measure Micro
------------------------------------------------------------
01 Leak 1.462
Precision 0.3333
Recall 0.1364
F1 0.1935
------------------------------------------------------------
Evaluate the single system output file '01.ann' against the gold standard file '01.ann' NER subtrack. Input files in BRAT format:
$> python evaluate.py brat ner gold/01.ann system/run1/01.ann
Report (SYSTEM: run1):
------------------------------------------------------------
Document ID Measure Micro
------------------------------------------------------------
01 Leak 1.462
Precision 0.3333
Recall 0.1364
F1 0.1935
------------------------------------------------------------
Evaluate the set of system outputs in the folder system/run1 against the set of gold standard annotations in gold/ using the SPANS subtrack. Input files in i2b2 format.
$> python evaluate.py i2b2 spans gold/ system/run1/
Report (SYSTEM: run1):
------------------------------------------------------------
SubTrack 2 [strict] Measure Micro
------------------------------------------------------------
Total (15 docs) Precision 0.3468
Recall 0.1239
F1 0.1826
------------------------------------------------------------
Report (SYSTEM: run1):
------------------------------------------------------------
SubTrack 2 [merged] Measure Micro
------------------------------------------------------------
Total (15 docs) Precision 0.469
Recall 0.1519
F1 0.2294
------------------------------------------------------------
Evaluate the set of system outputs in the folder system/run1, system/run2 and in the folder system/run3 against the set of gold standard annotations in gold/ using the NER subtrack. Input files in BRAT format.
$> python evaluate.py brat ner gold/ system/run1/ system/run2/ system/run3/
Report (SYSTEM: run1):
------------------------------------------------------------
SubTrack 1 [NER] Measure Micro
------------------------------------------------------------
Total (15 docs) Leak 1.369
Precision 0.3258
Recall 0.1239
F1 0.1795
------------------------------------------------------------
Report (SYSTEM: run2):
------------------------------------------------------------
SubTrack 1 [NER] Measure Micro
------------------------------------------------------------
Total (15 docs) Leak 1.462
Precision 0.3333
Recall 0.1364
F1 0.1935
------------------------------------------------------------
Report (SYSTEM: run3):
------------------------------------------------------------
SubTrack 1 [NER] Measure Micro
------------------------------------------------------------
Total (15 docs) Leak 1.6
Precision 0.4
Recall 0.1429
F1 0.2105
------------------------------------------------------------
Aitor Gonzalez-Agirre (aitor.gonzalez@bsc.es)
Copyright (c) 2019 Secretaría de Estado para el Avance Digital (SEAD)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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