Workshop-NeuralODE-2020

A 30-minute showcase on the how and the why of neural differential equations.

Content

There are three julia notebooks that show,

Notebook 1: an introduction to machine learning and neural networks,

Notebook 2: learning reaction kinetics using neural differential equations (NODEs),

Notebook 3: coupling these NODEs with reactor models.

Installation instructions

Installing Julia

1. Download the Julia binaries for your system here we suggest to install the Long-term support release, v1.0.5
2. Yes, it is that simple ⚡

Installing IJulia

Then run the Julia application (double-click on it); a window with a julia> prompt will appear. At the prompt, type:

using Pkg
Pkg.add("IJulia")

to install IJulia.

This process installs a kernel specification that tells Jupyter (or JupyterLab) etcetera how to launch Julia.

Pkg.add("IJulia") does not actually install Jupyter itself. You can install Jupyter if you want, but it can also be installed automatically when you run IJulia.notebook() below. (You can force it to use a specific jupyter installation by setting ENV["JUPYTER"] to the path of the jupyter program before Pkg.add, or before running Pkg.build("IJulia"); your preference is remembered on subsequent updates.

Installing the packages (first time running workshop)

After downloading Julia clone/download this repository to a location of your choice. Then start Julia. For linux/MAC users just use the command line and navigate to your local copy of the repository. For windows users copy the path to the repository and navigate Julia to that directory as follows, type ";" to go to the bash shell (red),

cd /change/this/to/the/location/of/Workshop-NeuralODE-2020 

Now that Julia has been navigated to the right working directory regardless of the operating system we can start the workshop.

In the normal Julia shell (green), activate the package and install the right packages. This can take a few minutes.

import Pkg
Pkg.activate(".")
Pkg.instantiate()  # only the first time you run this environment

After a succesful installation of the packages the jupyter notebooks can be started.

Running the notebook

type the following in Julia, at the julia> prompt:

import Pkg
Pkg.activate(".")
using IJulia
notebook()

to launch the IJulia notebook in your browser.

The first time you run notebook(), it will prompt you for whether it should install Jupyter. Hit enter to have it use the Conda.jl package to install a minimal Python+Jupyter distribution (via Miniconda) that is private to Julia (not in your PATH). On Linux, it defaults to looking for jupyter in your PATH first, and only asks to installs the Conda Jupyter if that fails; you can force it to use Conda on Linux by setting ENV["JUPYTER"]="" during installation (see above). (In a Debian or Ubuntu GNU/Linux system, install the package jupyter-client to install the system jupyter.)

source

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Contact: Bram.De.Jaegher@gmail.com