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How to set up a DEV environment

Required Python version >= 3.6

Setting up the environment with pipenv

pipenv is a utility that manages virtual environments and pip dependencies at the same time. To install it, navigate to the project's root directory and run:

pip3 install pipenv

This will make sure that pipenv uses your latest version of Python3, which is hopefully 3.6 or higher. Please refer to the official website for more information on pipenv.

A Makefile has been created for convenience, so that you can install the project dependencies, download the required models, test and build the tool easily.

Makefile specifications

To install all of the required packages for development and testing run:

make install

The tool will not run without an English language model and a tagger. To download spacy's English language model and NLTK's default tagger run:

make download_models

To execute the unit tests run:

make test

Code quality checks can be run with:

make lint

A wheel distribution of this tool can be created with:

make dist

How to write your own NER model

NERDS is a framework that provides some NER capabilities - among which the option of creating ensembles of NER models - but primarily made to be extended. In the following sections we take a look at the basic data exchange classes, and how you can use them to create your own models.

Understanding the main data exchange classes

There are 3 main classes in the nerds.core.model.input.* package that are used in our NER models: Document, Annotation and AnnotatedDocument.

A Document class is the abstract representation of a raw document. It should always implement the plain_text_ attribute, that returns the plain text representation of the object, as it's the one where we are going to perform NER. Therefore, whenever we want to process any new type of document format - XML, PDF, JSON, brat, etc. - the only requirement is to write an adapter that reads the file(s) from an input directory and transforms them to Document objects. The default Document object works seamlessly with .txt files.

The Annotation class contains the data for a single annotation. This is the text (e.g. "fox"), the label (e.g. "ANIMAL") and the offsets that correspond to offsets in the plain_text_ representation of a Document (e.g. 40-42).

Important to note: The offsets is a 2-tuple of integers that represent the position of the first and the last character of the annotation. Be careful, because some libraries end the offset one character after the final character i.e. at start_offset + len(word). This is not the case with us, we currently end the offsets at exactly the final character i.e. at start_offset + len(word) - 1.

Finally, the AnnotatedDocument class is a combination of Document and a list of Annotation, and it can represent two things:

  • Ground truth data (e.g. brat annotation files).
  • Predictions on documents after they run through our NER models.

The AnnotatedDocument class exposes the annotated_text_ attribute which returns the plain text representation of the document with inline annotations.

Extending the base model class

The basic class that every model needs to extend is the NERModel class in the nerds.core.model.ner.base package. The model class implements a fit - transform API, similarly to sklearn. To implement a new model, one must extend the following methods at minimum:

  • fit: Trains a model given a list of AnnotatedDocument objects.
  • transform: Gets a list of Document objects and transforms them to AnnotatedDocument.
  • save: Disk persistence of a model.
  • load: Disk persistence of a model.

Please note that all of the class methods, utility functions, etc. should operate on Document and AnnotatedDocument objects, to maintain compatibility with the rest of the framework. The only exception is "private" methods used internally in classes.

Running experiments

So, let's assume you have a dataset that contains annotated text. If it's in a format that is already supported (e.g. brat), then you may just load it into AnnotatedDocument objects using the built-in classes. Otherwise, you will have to extend the nerds.core.model.input.DataInput class to support the format. Then, you may use the built-in NER models (or create your own) either alone, or in an ensemble and evaluate their predictive capabilities on your dataset.

In the nerds.core.model.evaluate package, there are helper methods and classes to perform k-fold cross-validation. Please, refer to the nerds.examples package where you may look at working code examples with real datasets.

Contributing to the project

New models and input adapters are always welcome. Please make sure your code is well-documented and readable. Before creating a pull request make sure:

  • make test shows that all the unit test pass.
  • make lint shows no Python code violations.
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