galahad 0.1.0.dev0
Machine learning model server that can predict AND train
License: Apache License 2.0
Requires Python: >=3.7.0
Keywords: inception

# galahad

<a href='https://inception-galahad.readthedocs.io/en/latest'>
    <img src='https://readthedocs.org/projects/inception-galahad/badge/?version=latest' alt='Documentation Status' />
</a>


Machine learning model server for NLP that can predict AND train. It can be e.g. used for interactive machine
learning setups or as an external recommender with [INCEpTION](https://inception-project.github.io/).
It provides a REST-like interface and hence is integrable with a wide range of applications and use cases.

## Installation

You can install the newest version via

    pip install galahad

## Usage

`galahad` is a server-based application that uses [FastApi](https://fastapi.tiangolo.com/)
in the background. To get started, create a Python script like the one below.

    import logging
    
    import uvicorn
    
    from galahad.server import GalahadServer
    from galahad.server.contrib.ner.spacy_ner import SpacyNerTagger
    from galahad.server.contrib.pos.spacy_pos import SpacyPosTagger
    from galahad.server.contrib.sentence_classification.sklearn_sentence_classifier import SklearnSentenceClassifier
    
    server = GalahadServer("my_data_folder")
    server.add_classifier("SpacyPOS", SpacyPosTagger("en_core_web_sm"))
    server.add_classifier("SpacyNER", SpacyNerTagger("en_core_web_sm"))
    server.add_classifier("Sent", SklearnSentenceClassifier())
    
    
    if __name__ == "__main__":
        logging.basicConfig(format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', level=logging.DEBUG)
    
        uvicorn.run(server, host="127.0.0.1", port=8000)

This starts `galahad` so that you can use it e.g. together with the `galahad` client
or as a recommender in [INCEpTION](https://inception-project.github.io/).

Alternatively, you can run it on the command line via `uvicorn main:server`, where `main` is the name of your script 
(in this case, *main.py*) and `server` the name of your `GalahadServer` variable.

## API documentation

When running a Galahad instance, you can view the REST API documentation on http://localhost:8000/redoc .

## Examples

`galahad` can be used with a wide range of different clients. A few examples are described in the following:

### INCEpTION

[INCEpTION](https://inception-project.github.io/) is a semantic annotation platform offering intelligent 
assistance and knowledge management. It is widely used in the NLP community for annotating text.
`galahad` can be used to provide annotation suggestions to improve annotation speed and quality.
These can either be static or dynamic. For the latter, `galahad` models are trained and updated during annotation
to provide better suggestions the more data is annotated.

In order to connect INCEpTION and `galahad`, you first need to write a server Python script like above. add models to
your server and then run it. In INCEpTION, in your project, go to the recommender settings.
Add a external recommender V2 to INCEpTION, check the server connection and then select a classifer
from the list. You are now ready to annotate!

<p align="center">
  <img src="https://raw.githubusercontent.com/inception-project/inception-external-recommender-v2/main/img/galahad_inception.gif" />
</p>

As an example, here we annotate named entities and use a pre-trained [Spacy](https://spacy.io/) model.
Gray are recommendations and red are real annotations. Annotators can accept, reject or ignore suggestions
made by Galahad.

<p align="center">
  <img src="https://raw.githubusercontent.com/inception-project/inception-external-recommender-v2/main/img/inception_galahad_ner.png" />
</p>

### Gradio

After starting a Galahad instance, you can visualize the predictions of pretrained models via
[Gradio](https://gradio.app/). For that, just run 

    python examples/gradio_demo.py TASK_NAME

We currently support part-of-speech tagging (`pos`) and named entity recognition (`ner`) as tasks.

<p align="center">
  <img src="https://raw.githubusercontent.com/inception-project/inception-external-recommender-v2/main/img/gradio_ner.png" alt="Gradio named entity recognition demo"/>
</p>

### Python client

Galahad comes with a Python client that you can use to programmatically access the API without worrying about the 
underlying protocol. Please refer to the API documentation of Galahad that describes how to use it.

## Architecture

Galahad works on the basis of *datasets*, *documents*, *classifiers*, *models*, **annotations**.

- **Document**: A document contains the text and annotations. 
- **Dataset**: a dataset groups annotated documents together, representing e.g. an annotated corpus.
- **Classifier**: A classifier is a machine learning algorithm that can be used to make predictions and can be optionally
  be trained. The result of training is called the *model*. There can be multiple models for each classifier, e.g. one
  per user. 
- **Annotations**: Annotations consist of a type and features. Annotations can either represent spans by having a begin
  and end feature that points into the text or be standalone.

### Document representation

Documents are represented as JSON objects. They have a text, a version and annotations. Annotations are grouped by 
their type. An example document looks like the following:

```json
{
    "text": "Joe waited for the train . The train was late .",
    "version": 23,
    "annotations": {
        "t.token": [
            {"begin": 0, "end": 3},
            {"begin": 4, "end": 10},
            {"begin": 11, "end": 14},
            {"begin": 15, "end": 18},
            {"begin": 19, "end": 24},
            {"begin": 25, "end": 26},
            {"begin": 27, "end": 30},
            {"begin": 31, "end": 36},
            {"begin": 37, "end": 40},
            {"begin": 41, "end": 45},
            {"begin": 46, "end": 47}
        ],
        "t.sentence": [
            {"begin": 0, "end": 26},
            {"begin": 27, "end": 47}
        ],
        "t.named_entity": [
            {"begin": 0, "end": 3, "features": {"f.value": "PER"}}
        ]
    }
}
```

### Disk layout

Galahad stores datasets, documents and models on disk. The layout looks like the following:

    data
    ├───datasets
    │   └───dataset1
    │       └───document1
    │       └───document2
    │   └───dataset2
    ├───locks
    ├───models
    │   └───classifier1
    │   └───classifier2

We also plan to add additional store alternatives to Galahad, for instance SQLite.

### Classifier training

Classifier training is done by creating a new process that then takes over the training. This is needed because of the
GIL in Python. If we did not do this, then the main thread would be blocked and the web app could not respond to new requests.
Also, only one model could be trained at the time. 

When the request to train a classifier arrives, it is first checked whether training is not already
running. Training the same classifier twice at the same time is prevented by using file locks.

## Development

The required dependencies are managed by **pip**. A virtual environment
containing all needed packages for development and production can be
created and activated by

    python3 -m venv venv
    source venv/bin/activate
    pip install -e ".[all]"
    make get_test_dependencies