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deep-learning-health-life-sciences

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Workshop on Deep Learning for Health and Life Sciences

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# Deep Learning for Health and Life Sciences with ![pytorch-logo](https://raw.githubusercontent.com/leriomaggio/deep-learning-health-life-sciences/master/pytorch_logo_small.png)

This workshop has been presented at the [**Data Week Online 2020**](http://www.bristol.ac.uk/golding/get-involved/data-week-online-2020/) organised by the [**Jean Golding Insitute**](http://www.bristol.ac.uk/golding/)

![JGI Logo](https://raw.githubusercontent.com/leriomaggio/deep-learning-health-life-sciences/master/logos/jgi-logo.png "Jean Golding Institute")
![UoB Logo](https://raw.githubusercontent.com/leriomaggio/deep-learning-health-life-sciences/master/logos/uob_logo_small.png "University of Bristol")

The introductory deck of slides to this tutorial is available on my [SpeakerDeck](https://speakerdeck.com/leriomaggio/) profile:

[Deep Learning for the Health and Life Sciences with PyTorch](https://speakerdeck.com/leriomaggio/deep-learning-for-health-and-life-sciences-with-pytorch).

The **full abstract** of the workshop is available here: [Abstract](./abstract.md)

### Content at a glance

* Introduction to ML and DL for the Health and Life Science
	- Short introduction to PyTorch

* Reproducibility and Replicability
	- Replication Case study on Heart Failure

* BioImages
	- Diabetic Retinopathy from fundus images
	- Histopathological Images and Transfer Learning

* Few Notes on Model Interpretability

### Technical Requirements

This tutorial runs on ***\*Python 3\**** (Py3.4+ should be fine), and requires the following main packages:

- `numpy`
- `scipy`
- `matplotlib`
- `scikit-learn`
- `torch` (of course 😄)
- `torchvision`

The complete list of requirements is available in [`requirements.txt`](./requirements.txt)

Detailed (**step-by-step**) instructions to setup the Python virtual environment on your local machine are also available [here](./setup.md).

If you don't want to bother setting up everything on your local computer (__and also have a pretty good internet connection_) you might also consider the following two alternatives:

#### MyBinder

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/leriomaggio/deep-learning-health-life-sciences/master)

#### Google Colab

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/leriomaggio/deep-learning-heath-life-sciences)

### License Summary

The material provided in this repository adopts two different licence files, for Lecture notes and Source Code, respectively.

The Lecture notes (and corresponding source notebooks) are licensed under <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/80x15.png" /></a><br /> <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.

The samples and reference code within this repository is made available under the **GNU GPL v3**.

See the `LICENSE` file.

#### References

**Author**: Valerio Maggio, **Senior Research Associate** `@` Dynamic Genetics Lab

| **Contacts** |
| ------------ |
|  <img src="logos/twitter_small.png" alt="Twitter" style="display:inline"/> [`@leriomaggio`](http://twitter.com/leriomaggio) |
|       <img src="logos/linkedin_small.png" alt="LinkedIn" style="display:inline"/> [`ValerioMaggio`](http://it.linkedin.com/in/valeriomaggio)       |
|       <img src="logos/gmail_small.png" alt="Mail" style="display:inline"/> [`valerio.maggio@bristol.ac.uk`](valerio.maggio@bristol.ac.uk)         |

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