# Extraction Module

The *Extraction Module* is divided into four components. The first three are pages dedicated to simple extraction processes on various data types (images, text notes, and time series) using pre-trained models and/or *Python* libraries. The fourth component is [*MEDimage*](https://medimage.readthedocs.io/en/latest/index.html), which is the implementation of a *Python* open-source package designed for medical image processing and radiomics features extraction.

{% hint style="info" %}
In the video below, the "HAIM study" refers to [the study of Soenksen et al.](https://www.nature.com/articles/s41746-022-00689-4)
{% endhint %}

{% embed url="<https://youtu.be/eNKN7H9nwjc?si=zzTJjwQgApcLwKxu>" %}
Extraction Module Video Tutorial
{% endembed %}

**Content**

* [00:00](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=0s) Overview&#x20;
* [00:50](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=50s) Extraction Images&#x20;
* [04:24](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=264s) Extraction Time Series
* [08:29](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=509s) Extraction Text&#x20;
* [10:48](https://www.youtube.com/watch?v=eNKN7H9nwjc\&t=648s) Last Word

**Data**

* Physionet : <https://physionet.org/>&#x20;
* MIMIC-IV Demo database : <https://physionet.org/content/mimic-iv-demo/2.2/>&#x20;
* MIMIC-IV-Note : <https://physionet.org/content/mimic-iv-note/2.2/>&#x20;
* MIMIC-IV-CXR : <https://physionet.org/content/mimic-cxr-jpg/2.0.0/>&#x20;
* Study of Soenksen et al. : <https://www.nature.com/articles/s41746-022-00689-4>&#x20;

**Extraction tools**

* TorchXRayVision : <https://github.com/mlmed/torchxrayvision>
* TSfresh : <https://tsfresh.readthedocs.io>&#x20;
* BioBERT : <https://arxiv.org/abs/1901.08746>
* BioBERT weights : <https://github.com/EmilyAlsentzer/clinicalBERT>&#x20;

***

{% content-ref url="extraction-modules/image-extraction-page" %}
[image-extraction-page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/image-extraction-page)
{% endcontent-ref %}

{% content-ref url="extraction-modules/text-extraction-page" %}
[text-extraction-page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/text-extraction-page)
{% endcontent-ref %}

{% content-ref url="extraction-modules/time-series-extraction-page" %}
[time-series-extraction-page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/time-series-extraction-page)
{% endcontent-ref %}

{% content-ref url="extraction-modules/medimage" %}
[medimage](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/medimage)
{% endcontent-ref %}
