This repository was born out of research on machine learning for particle physics done for David Miller at The University of Chicago. I intend it to be for those continuing similar research for professor Miller at UChicago. Hopefully, it will serve as a guide for how to set up the tools you need as well as how to run them on data in the formats that were given to me.

The goal of this Github repository is to train images of JZ0W (background) interactions and ZvvHbb (signal) interactions using Deep Learning such that we will be able to distinguish the two effectively. It will contain A visualization notebook, a training notebook, a python file with convenient functions defined, and all of the data that I used.

The notebooks display and clean the data (format it from hdf5 to numpy, remove 0 values in images, and add labels). Then the data is shuffled and passed to a Convolution Neural Netork model to train the data. Finally, they look at the accuracy and loss of the CNN model and plot ROC curves to get a better sense of how the model is doing.

For formatting the data I used a former graduate students code to deal with the structure of the data. It was originally in nTuple form and this graduate student's code formatted it from nTuples to hdf5 files such that the data was organized more clearly. It can be found on his Github here and it is the gFEXtuple2hdf5.py file. I made slight edits to the code to deal with the slightly different formatting of the data I was using. The code linked above formats the data into a 24x32 shape, whilst I shaped it into a 28x32 shape -- this was simply had to do with what section of the data we were looking at.

To use the code to convert nTuple data to hdf5 files, you will need to install ROOT. This can be extremely tricky and time consuming if your environment is not set up correctly and you don't know what you are doing. But if you get through it, you will need to make sure that the python extension is also installed to use this code.

A nice work around (although it presents it's own unique challenges) is to use Tier 3 -- ask David for an account. They have their own way of installing packages using something called lcgenv

Here are some commands I found to be useful to set up my environment, and to transfer files to and from Tier 3 once I ssh'ed into my Tier 3 account. For set up:

setupATLAS # initial setup (gets lsetup command)

lsetup "lcgenv -p LCG_86 x86_64-slc6-gcc62-opt" # to see possible packages

lsetup "lcgenv -p LCG_86 x86_64-slc6-gcc62-opt pip”. #set up pip


lsetup "lcgenv -p LCG_86 x86_64-slc6-gcc62-opt ROOT" #set up ROOT

pip install --user numpy root-numpy ... # can then pip install other libraries ((matplotlib doesn’t work with this!))

  # then on future set ups, I can just do 

lsetup "lcgenv -p LCG_86 x86_64-slc6-gcc62-opt pip" 

In order to transfer files between the Tier 3 and your own computer you will need to use the SCP command: scp /path/to/file username@a:/path/to/destinationand the reverese command to send files back to your own computer for visualization and training. As far as Tier 3 and ROOT goes this should set you up alright.

The Visualization Notebook is here so that you can see how and why the data is cleaned. It takes in the images initially, cuts off the buffer region (Rows of 0's), labels the data, combines the background and signal images, shuffles them, and then finally plots them

All of this is put in the images_and_labels function in the convert_python.py file so that it can all be done with one function call.

Some of the data preprocessing is done in this notebook. We need to convert our data into JPEG images for later use in something called DNNDK (Deep Neural Network Development Kit). This is another part of the project. All you need to know for the purposes of this notebook is that this requires a different input for our Network.

After formatting the data, this notebook trains the data using different Convolutional Neural Networks (CNN). This is done using Keras -- with Tensor Flow as the backend. For this notebook I used 4 different CNN's: 1 Convolutional Layer, 2 Convolutional Layers, 1 Convolutional Layer and 1 Max Pooling Layer, and 2 Convolutional Layers and 2 Max Pooling Layers.

Finally after training and comparing the Networks, we then convert this into a frozen graph that is used to create a TensorFlow graph which is required for the DNNDK.