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Machine Learning: Train a Neural Network

This tutorial demonstrates how to train a a multilayer perceptron for regression using SciKit-Learn.

1. Acquire Training Data

The data we use in this tutorial is taken from a recent model of small molecule adsorption to transition metal nanoparticles. Specifically, we use DFT-calculated values for the adsorption energy of ·CH3, CO, and ·OH radicals to Ag, Au, and Cu nanoparticles ranging in size from 55 to 172 atoms.

This File contains the data we will use in this tutorial. A sample of the first 5 lines in the file can be found below:

PBE_BE_eV CE_Local_eV ChemPot_eV MADS_eV
-1.39 -2.38 -4.96 -2.10
-1.11 -3.35 -4.96 -2.10
-0.95 -4.81 -4.96 -2.10
-0.74 -4.60 -4.96 -2.10

2. Upload the Training Data

In order to upload training data, we first click the Dropbox button in the left sidebar. This will bring us to the Dropbox Page. We can then click the "Upload" button, circled below:

Dropbox Page with Upload

Then, when the browser's upload window appears, we navigate to where we downloaded the file in section 1, and select it for upload. If the upload was successful, the file will then be visible in the dropbox.

Take note of the name of the file. For the purposes of this tutorial, it should be named data_to_train_with.csv

3. Copy the "Python ML Train" Workflow from the Workflow Bank

Next, we select theBank Worfklows button in the left sidebar, which brings us to the Bank Workflows Page. We then search for the "Python ML Train" workflow owned by the " Curators" account, and copy it to our account.

4. Create the ML Job

Next, we can create a new job by selecting the Create Job button in the left sidebar. This will bring us to a new job on the Job Designer page.

First, we will give the job a friendly name, such as "Python ML Tutorial" (see below). Then, we will click the Actions Button (the three vertical dots in the upper-right of the job designer), and choose "Select Workflow."

Job Designer with Circles

This will bring up the Select Workflow dialogue. We then search for "Python ML Train" and click on it to bring it into our account.

5. Configure the ML Workflow

We now have our ML workflow selected. Select the Workflows Tab, and we can see our training workflow.

We can see two subworkflows available: Set Up the Job and Machine Learning.

Specify the Training Data

We will first configure the Set Up the Job workflow to accept our training data.

Begin by selecting the "Declare Training Data" workflow unit, circled below:

ML Workflow Tab

We can now see the "Declare Training Data" IO unit. Because we named our file in dropbox data_to_train_with.csv earlier, we do not need to modify this unit. In a scenario where we wanted to use a different file name for our training data, the Workflow Designer could be used to modify the value.

Training Data IO Unit

A Word of Caution

The only modifications that should be made in the Set Up the Job subworkflow are the filenames in the "Declare Training Data" and "Declare Predict Data" IO units. The Set Up the Job subworkflow is automatically re-configured during the training process. Modifying other values, or adding/removing workflow units to this subworkflow, can disrupt creation of the Predict workflow.

We will then close the Declare Training Data IO unit by clicking on the "X" in the dialogue's upper right corner. This will bring us back to the Workflows Tab.


We can now configure our settings file. Begin by selecting the Machine Learning subworkflow. This will make visible all of the machine learning units that are inside the workflow:

ML Train

This workflow has the following steps:

  1. Setup Packages and Variables - Configures the job and downloads all required packages with pip
  2. Data Input - Reads the training data from disk
  3. Data Standardize - Scales the data such that it has mean 0 and standard deviation 1
  4. Model Train and Predict - Handles model training, and prediction
  5. Parity Plot - Draws a plot of model predictions versus training data, and saves it to the disk. This plot is shown on the Results tab.

We will configure the file by selecting the Setup Packages and Variables unit (see above figure). This will open a dialogue containing the content of Scroll down to line 41 of the file, and note the presence of a variable named target_column_name, with the value of "target". This value should instead be the target column of our training data, so change it to "PBE_BE_eV" as below:


Then, close the dialogue. We can now demonstrate how a workflow unit's parameters can be changed. For this tutorial, we will set our neural network to have 2 hidden layers of 100 layers each, and we will train for 5000 iterations.

Begin by selecting the ML Train and Predict workflow unit, as below:

ML Train and Predict

We can then scroll down to line 36, and change the hidden_layer_sizes argument from (100,) to (100,100) to add an extra hidden layer of 100 neurons each to the model. We can then find line 40, and adjust the max_iter argument from 500 to 5000, to give the network enough time to train. These changes are circled below.

Neural Network Settings

Then, close the dialogue. The workflow has now been configured, and we are ready to train.

6. Submit the Job

Click the check-mark in the upper right of the job designer, in the Header Menu to save the job. We now return to the job explorer page with the job in a pre-submission status.


We can now run the job and wait for it to complete.

7. Analyze the Training Results

After a few minutes, the job will complete. We can then visit the job's results tab, where we will see that two properties have been calculated. The first, Machine Learning - Model Train and Predict is the predict workflow that was generated by the machine learning job. The predict workflow can be used to leverage the trained model for additional predictions on new data.

The second result visible is Machine Learning - Parity Plot, which contains the predicted versus actual values for the adsorption energies we trained the model on.

Results Tab


This tutorial is demonstrated in the following animation: