QML Tutorial

This tutorial is a general introduction to kernel-ridge regression with QML.


Regression model of some property, \(y\), for some system, \(\widetilde{\mathbf{X}}\) - this could correspond to e.g. the atomization energy of a molecule:

\(y\left(\widetilde{\mathbf{X}} \right) = \sum_i \alpha_i \ K\left( \widetilde{\mathbf{X}}, \mathbf{X}_i\right)\)

E.g. Using Gaussian kernel function with Frobenius norm:

\(K_{ij} = K\left( \mathbf{X}_i, \mathbf{X}_j\right) = \exp\left( -\frac{\| \mathbf{X}_i - \mathbf{X}_j\|_2^2}{2\sigma^2}\right)\)

Regression coefficients are obtained through kernel matrix inversion and multiplication with reference labels

\(\boldsymbol{\alpha} = (\mathbf{K} + \lambda \mathbf{I})^{-1} \mathbf{y}\)

Tutorial exercises

Clone the following GIT repository to access the necessary scripts and QM7 dataset (atomization energies and relaxed geometries at PBE0/def2-TZVP level of theory) for ~7k GDB1-7 molecules. [1] [2]

git clone https://github.com/qmlcode/tutorial.git

Additionally, the repository contains Python3 scripts with the solutions to each exercise.

Exercise 1: Representations

In this exercise we use qml~to generate the Coulomb matrix and Bag of bonds (BoB) representations. [3] In QML data can be parsed via the Compound class, which stores data and generates representations in Numpy’s ndarray format. If you run the code below, you will read in the file qm7/0001.xyz (a methane molecule) and generate a coulomb matrix representation (sorted by row-norm) and a BoB representation.

import qml

# Create the compound object mol from the file qm7/0001.xyz which happens to be methane
mol = qml.Compound(xyz="qm7/0001.xyz")

# Generate and print a coulomb matrix for compound with 5 atoms
mol.generate_coulomb_matrix(size=5, sorting="row-norm")

# Generate and print BoB bags for compound containing C and H
mol.generate_bob(asize={"C":2, "H":5})

The representations are simply stored as 1D-vectors. Note the keyword size which is the largest number of atoms in a molecule occurring in test or training set. Additionally, the coulomb matrix can take a sorting scheme as keyword, and the BoB representations requires the specifications of how many atoms of a certain type to make room for in the representations.

Lastly, you can print the following properties which is read from the XYZ file:

# Print other properties stored in the object

Exercise 2: Kernels

In this exercise we generate a Gaussian kernel matrix, \(\mathbf{K}\), using the representations, \(\mathbf{X}\), which are generated similarly to the example in the previous exercise:

\(K_{ij} = \exp\left( -\frac{\| \mathbf{X}_i - \mathbf{X}_j\|_2^2}{2\sigma^2}\right)\)

QML supplies functions to generate the most basic kernels (E.g. Gaussian, Laplacian). In the exercise below, we calculate a Gaussian kernel for the QM7 dataset. In order to save time you can import the entire QM7 dataset as Compound objects from the file tutorial_data.py found in the tutorial GitHub repository.

# Import QM7, already parsed to QML
from tutorial_data import compounds

from qml.kernels import gaussian_kernel

# For every compound generate a coulomb matrix or BoB
for mol in compounds:

    mol.generate_coulomb_matrix(size=23, sorting="row-norm")
    # mol.generate_bob(size=23, asize={"O":3, "C":7, "N":3, "H":16, "S":1})

# Make a big 2D array with all the representations
X = np.array([mol.representation for mol in compounds])

# Print all representations

# Run on only a subset of the first 100 (for speed)
X = X[:100]

# Define the kernel width
sigma = 1000.0

# K is also a Numpy array
K = gaussian_kernel(X, X, sigma)

# Print the kernel
print K

Exercise 3: Regression

With the kernel matrix and representations sorted out in the previous two exercise, we can now solve the \(\boldsymbol{\alpha}\) regression coefficients:

\(\boldsymbol{\alpha} = (\mathbf{K} + \lambda \mathbf{I})^{-1} \mathbf{y}\label{eq:inv}\)

One of the most efficient ways of solving this equation is using a Cholesky-decomposition. QML includes a function named cho_solve() to do this via the math module qml.math. In this step it is convenient to only use a subset of the full dataset as training data (see below). The following builds on the code from the previous step. To save time, you can import the PBE0/def2-TZVP atomization energies for the QM7 dataset from the file tutorial_data.py. This has been sorted to match the ordering of the representations generated in the previous exercise. Extend your code from the previous step with the code below:

from qml.math import cho_solve
from tutorial_data import energy_pbe0

# Assign 1000 first molecules to the training set
X_training = X[:1000]
Y_training = energy_pbe0[:1000]

sigma = 4000.0
K = gaussian_kernel(X_training, X_training, sigma)

# Add a small lambda to the diagonal of the kernel matrix
K[np.diag_indices_from(K)] += 1e-8

# Use the built-in Cholesky-decomposition to solve
alpha = cho_solve(K, Y_training)


Exercise 4: Prediction

With the \(\boldsymbol{\alpha}\) regression coefficients from the previous step, we have (successfully) trained the machine, and we are now ready to do predictions for other compounds. This is done using the following equation:

\(y\left(\widetilde{\mathbf{X}} \right) = \sum_i \alpha_i \ K\left( \widetilde{\mathbf{X}}, \mathbf{X}_i\right)\)

In this step we further divide the dataset into a training and a test set. Try using the last 1000 entries as test set.

# Assign 1000 last molecules to the test set
X_test = X[-1000:]
Y_test = energy_pbe0[-1000:]

# calculate a kernel matrix between test and training data, using the same sigma
Ks = gaussian_kernel(X_test, X_training, sigma)

# Make the predictions
Y_predicted = np.dot(Ks, alpha)

# Calculate mean-absolute-error (MAE):
print np.mean(np.abs(Y_predicted - Y_test))

Exercise 5: Learning curves

Repeat the prediction from Exercise 2.4 with training set sizes of 1000, 2000, and 4000 molecules. Note the MAE for every training size. Plot a learning curve of the MAE versus the training set size. Generate a learning curve for the Gaussian and Laplacian kernels, as well using the coulomb matrix and bag-of-bonds representations. Which combination gives the best learning curve? Note you will have to adjust the kernel width (sigma) underway.

Exercise 6: Delta learning

A powerful technique in machine learning is the delta learning approach. Instead of predicting the PBE0/def2-TZVP atomization energies, we shall try to predict the difference between DFTB3 (a semi-empirical quantum method) and PBE0 atomization energies. Instead of importing the energy_pbe0 data, you can import the energy_delta and use this instead

from tutorial_data import energy_delta

Y_training = energy_delta[:1000]
Y_test = energy_delta[-1000:]

Finally re-draw one of the learning curves from the previous exercise, and note how the prediction improves.


[1]Rupp et al, Phys Rev Letters, 2012.
[2]Ruddigkeit et al, J Chem Inf Model, 2012.
[3]Montavon et al, New J Phys, 2013.