README.md

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license: cc-by-4.0
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# The Tokenizer for Clinical Cases Written in Spanish


## Introduction
This repository contains the tokenization model trained using the SPACCC_TOKEN corpus (https://github.com/PlanTL-SANIDAD/SPACCC_TOKEN). The model was trained using the 90% of the corpus (900 clinical cases) and tested against the 10% (100 clinical cases). This model is a great resource to tokenize biomedical documents, specially clinical cases written in Spanish.

This model was created using the Apache OpenNLP machine learning toolkit (https://opennlp.apache.org/), with the release number 1.8.4, released in December 2017.

This repository contains the training set, testing set, Gold Standard.

## Prerequisites
This software has been compiled with Java SE 1.8 and it should work with recent versions. You can download Java from the following website: https://www.java.com/en/download

The executable file already includes the Apache OpenNLP dependencies inside, so the download of this toolkit is not necessary. However, you may download the latest version from this website: https://opennlp.apache.org/download.html

The library file we have used to compile is "opennlp-tools-1.8.4.jar". The source code should be able to compile with the latest version of OpenNLP, "opennlp-tools-*RELEASE_NUMBER*.jar". In case there are compilation or execution errors, please let us know and we will make all the necessary updates.

## Directory structure
<pre>
exec/
  An executable file that can be used to apply the tokenization to your documents.
  You can find the notes about its execution below in section "Usage".

gold_standard/

  The clinical cases used as gold standard to evaluate the model's performance.



model/

  The tokenizationint model, "es-tokenization-model-spaccc.bin", a binary file.



src/

  The source code to create the model (CreateModelTok.java) and evaluate it (EvaluateModelTok.java).

  The directory includes an example about how to use the model inside your code (Tokenization.java).

  File "abbreviations.dat" contains a list of abbreviations, essential to build the model.



test_set/
  The clinical cases used as test set to evaluate the model's performance.

train_set/

  The clinical cases used to build the model. We use a single file with all documents present in

  directory "train_set_docs" concatented.



train_set_docs/

  The clinical cases used to build the model. For each record the sentences are already splitted.



</pre>



## Usage

The executable file *Tokenizer.jar* is the program you need to tokenize the text in your document. For this program, two arguments are needed: (1) the text file to tokenize, and (2) the model file (*es-tokenization-model-spaccc.bin*). The program will display all tokens in the terminal, with one token per line.



From the `exec` folder, type the following command in your terminal:



<pre>

$ java -jar Tokenizer.jar INPUT_FILE MODEL_FILE

</pre>



## Examples



Assuming you have the executable file, the input file and the model file in the same directory:

<pre>

$ java -jar Tokenizer.jar file.txt es-tokenizer-model-spaccc.bin

</pre>



## Model creation

To create this tokenization model, we used the following training parameters (class *TrainingParameters* in OpenNLP) to get the best performance:

- Number of iterations: 1500.

- Cutoff parameter: 4.

- Trainer type parameter: *EventTrainer.EVENT_VALUE*.

- Algorithm: Maximum Entropy (*ModelType.MAXENT.name()*).



Meanwhile, we used the following parameters for the tokenizer builder (class *TokenizerFactory* in OpenNLP) to get the best performance:
- Language code: *es* (for Spanish).
- Abbreviation dictionary: file "abbreviations.dat" (included in the `src/` directory).
- Use alphanumeric optimization: false
- Alphanumeric pattern: null

## Model evaluation

After tuning the model using different values for each parameter mentioned above, we got the best performance with the values mentioned above.

|      | Value |
| ----------------------------------------: | :------ |
| Number of tokens in the gold standard | 38247   |
| Number of tokens generated            | 38227   |
| Number of words correctly tokenized   | 38182   |
| Number of words wrongly tokenized     | 35     |
| Number of tokens missed     |   30   |
| **Precision**                                | **99.88%** |
| **Recall**                                   | **99.83%** |
| **F-Measure**                                | **99.85%**|

Table 1: Evaluation statistics for the tokenization model.


## Contact

Ander Intxaurrondo ([email protected])


## License

<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.

Copyright (c) 2018 Secretaría de Estado para el Avance Digital (SEAD)