Nuclear Talent course on Machine Learning in Nuclear Experiment and Theory

Introduction

Our emphasis throughout this series of lectures is on understanding the mathematical aspects of different algorithms used in the fields of data analysis and machine learning.

However, where possible we will emphasize the importance of using available software. We start thus with a hands-on and top-down approach to machine learning. The aim is thus to start with relevant data or data we have produced and use these to introduce statistical data analysis concepts and machine learning algorithms before we delve into the algorithms themselves. The examples we will use in the beginning, start with simple polynomials with random noise added. We will use the Python software package Scikit-Learn and introduce various machine learning algorithms to make fits of the data and predictions. We move thereafter to more interesting cases such as data from say experiments (below we will look at experimental nuclear binding energies as an example). These are examples where we can easily set up the data and then use machine learning algorithms included in for example Scikit-Learn.

These examples will serve us the purpose of getting started. Furthermore, they allow us to catch more than two birds with a stone. They will allow us to bring in some programming specific topics and tools as well as showing the power of various Python libraries for machine learning and statistical data analysis.

Although we have projects where you write your own codes, we will also focus on two specific Python packages for Machine Learning, Scikit-Learn and Tensorflow with Keras (see below for links etc). Moreover, the examples we introduce will serve as inputs to many of our discussions later, as well as allowing you to set up models and produce your own data and get started with programming.

AI/ML and some statements you may have heard (and what do they mean?)

1. Fei-Fei Li on ImageNet: map out the entire world of objects (The data that transformed AI research)
2. Russell and Norvig in their popular textbook: relevant to any intellectual task; it is truly a universal field (Artificial Intelligence, A modern approach)
3. Woody Bledsoe puts it more bluntly: in the long run, AI is the only science (quoted in Pamilla McCorduck, Machines who think)

If you wish to have a critical read on AI/ML from a societal point of view, see Kate Crawford's recent text Atlas of AI

What is Machine Learning?

Statistics, data science and machine learning form important fields of research in modern science. They describe how to learn and make predictions from data, as well as allowing us to extract important correlations about physical process and the underlying laws of motion in large data sets. The latter, big data sets, appear frequently in essentially all disciplines, from the traditional Science, Technology, Mathematics and Engineering fields to Life Science, Law, education research, the Humanities and the Social Sciences.

It has become more and more common to see research projects on big data in for example the Social Sciences where extracting patterns from complicated survey data is one of many research directions. Having a solid grasp of data analysis and machine learning is thus becoming central to scientific computing in many fields, and competences and skills within the fields of machine learning and scientific computing are nowadays strongly requested by many potential employers. The latter cannot be overstated, familiarity with machine learning has almost become a prerequisite for many of the most exciting employment opportunities, whether they are in bioinformatics, life science, physics or finance, in the private or the public sector. This author has had several students or met students who have been hired recently based on their skills and competences in scientific computing and data science, often with marginal knowledge of machine learning.

Machine learning is a subfield of computer science, and is closely related to computational statistics. It evolved from the study of pattern recognition in artificial intelligence (AI) research, and has made contributions to AI tasks like computer vision, natural language processing and speech recognition. Many of the methods we will study are also strongly rooted in basic mathematics and physics research.

Ideally, machine learning represents the science of giving computers the ability to learn without being explicitly programmed. The idea is that there exist generic algorithms which can be used to find patterns in a broad class of data sets without having to write code specifically for each problem. The algorithm will build its own logic based on the data. You should however always keep in mind that machines and algorithms are to a large extent developed by humans. The insights and knowledge we have about a specific system, play a central role when we develop a specific machine learning algorithm.

Machine learning is an extremely rich field, in spite of its young age. The increases we have seen during the last three decades in computational capabilities have been followed by developments of methods and techniques for analyzing and handling large date sets, relying heavily on statistics, computer science and mathematics. The field is rather new and developing rapidly. Popular software packages written in Python for machine learning like Scikit-learn, Tensorflow, PyTorch and Keras, all freely available at their respective GitHub sites, encompass communities of developers in the thousands or more. And the number of code developers and contributors keeps increasing. Not all the algorithms and methods can be given a rigorous mathematical justification, opening up thereby large rooms for experimenting and trial and error and thereby exciting new developments. However, a solid command of linear algebra, multivariate theory, probability theory, statistical data analysis, understanding errors and Monte Carlo methods are central elements in a proper understanding of many of algorithms and methods we will discuss.

Types of Machine Learning

The approaches to machine learning are many, but are often split into two main categories. In supervised learning we know the answer to a problem, and let the computer deduce the logic behind it. On the other hand, unsupervised learning is a method for finding patterns and relationship in data sets without any prior knowledge of the system. Some authours also operate with a third category, namely reinforcement learning. This is a paradigm of learning inspired by behavioral psychology, where learning is achieved by trial-and-error, solely from rewards and punishment.

Another way to categorize machine learning tasks is to consider the desired output of a system. Some of the most common tasks are:

• Classification: Outputs are divided into two or more classes. The goal is to produce a model that assigns inputs into one of these classes. An example is to identify digits based on pictures of hand-written ones. Classification is typically supervised learning.
• Regression: Finding a functional relationship between an input data set and a reference data set. The goal is to construct a function that maps input data to continuous output values.
• Clustering: Data are divided into groups with certain common traits, without knowing the different groups beforehand. It is thus a form of unsupervised learning.

Essential elements of ML

The methods we cover have three main topics in common, irrespective of whether we deal with supervised or unsupervised learning.

• The first ingredient is normally our data set (which can be subdivided into training, validation and test data). Many find the most difficult part of using Machine Learning to be the set up of your data in a meaningful way.
• The second item is a model which is normally a function of some parameters. The model reflects our knowledge of the system (or lack thereof). As an example, if we know that our data show a behavior similar to what would be predicted by a polynomial, fitting our data to a polynomial of some degree would then determin our model.
• The last ingredient is a so-called cost/loss function (or error or risk function) which allows us to present an estimate on how good our model is in reproducing the data it is supposed to train.

An optimization/minimization problem

At the heart of basically all Machine Learning algorithms we will encounter so-called minimization or optimization algorithms. A large family of such methods are so-called gradient methods.

A Frequentist approach to data analysis

When you hear phrases like predictions and estimations and correlations and causations, what do you think of? May be you think of the difference between classifying new data points and generating new data points. Or perhaps you consider that correlations represent some kind of symmetric statements like if $A$ is correlated with $B$, then $B$ is correlated with $A$. Causation on the other hand is directional, that is if $A$ causes $B$, $B$ does not necessarily cause $A$.

These concepts are in some sense the difference between machine learning and statistics. In machine learning and prediction based tasks, we are often interested in developing algorithms that are capable of learning patterns from given data in an automated fashion, and then using these learned patterns to make predictions or assessments of newly given data. In many cases, our primary concern is the quality of the predictions or assessments, and we are less concerned about the underlying patterns that were learned in order to make these predictions.

In machine learning we normally use a so-called frequentist approach, where the aim is to make predictions and find correlations. We focus less on for example extracting a probability distribution function (PDF). The PDF can be used in turn to make estimations and find causations such as given $A$ what is the likelihood of finding $B$.

What is a good model?

In science and engineering we often end up in situations where we want to infer (or learn) a quantitative model $M$ for a given set of sample points $\boldsymbol{X} \in [x_1, x_2,\dots x_N]$.

As we will see repeatedely in these lectures, we could try to fit these data points to a model given by a straight line, or if we wish to be more sophisticated to a more complex function.

The reason for inferring such a model is that it serves many useful purposes. On the one hand, the model can reveal information encoded in the data or underlying mechanisms from which the data were generated. For instance, we could discover important corelations that relate interesting physics interpretations.

In addition, it can simplify the representation of the given data set and help us in making predictions about future data samples.

A first important consideration to keep in mind is that inferring the correct model for a given data set is an elusive, if not impossible, task. The fundamental difficulty is that if we are not specific about what we mean by a correct model, there could easily be many different models that fit the given data set equally well.

What is a good model? Can we define it?

The central question is this: what leads us to say that a model is correct or optimal for a given data set? To make the model inference problem well posed, i.e., to guarantee that there is a unique optimal model for the given data, we need to impose additional assumptions or restrictions on the class of models considered. To this end, we should not be looking for just any model that can describe the data. Instead, we should look for a model $M$ that is the best among a restricted class of models. In addition, to make the model inference problem computationally tractable, we need to specify how restricted the class of models needs to be. A common strategy is to start with the simplest possible class of models that is just necessary to describe the data or solve the problem at hand. More precisely, the model class should be rich enough to contain at least one model that can fit the data to a desired accuracy and yet be restricted enough that it is relatively simple to find the best model for the given data.

Thus, the most popular strategy is to start from the simplest class of models and increase the complexity of the models only when the simpler models become inadequate. For instance, if we work with a regression problem to fit a set of sample points, one may first try the simplest class of models, namely linear models, followed obviously by more complex models.

How to evaluate which model fits best the data is something we will come back to over and over again in these sets of lectures.

Software and needed installations

We will make extensive use of Python as programming language and its myriad of available libraries. You will find Jupyter notebooks invaluable in your work. You can run R codes in the Jupyter/IPython notebooks, with the immediate benefit of visualizing your data. You can also use compiled languages like C++, Rust, Julia, Fortran etc if you prefer. The focus in these lectures will be on Python.

If you have Python installed (we strongly recommend Python3) and you feel pretty familiar with installing different packages, we recommend that you install the following Python packages via pip as

1. pip install numpy scipy matplotlib ipython scikit-learn mglearn sympy pandas pillow

For Python3, replace pip with pip3.

For OSX users we recommend, after having installed Xcode, to install brew. Brew allows for a seamless installation of additional software via for example

1. brew install python3

For Linux users, with its variety of distributions like for example the widely popular Ubuntu distribution, you can use pip as well and simply install Python as

1. sudo apt-get install python3 (or python for pyhton2.7)

etc etc.

Python installers

If you don't want to perform these operations separately and venture into the hassle of exploring how to set up dependencies and paths, we recommend two widely used distrubutions which set up all relevant dependencies for Python, namely

• Anaconda,

which is an open source distribution of the Python and R programming languages for large-scale data processing, predictive analytics, and scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.

• Enthought canopy

is a Python distribution for scientific and analytic computing distribution and analysis environment, available for free and under a commercial license.

Furthermore, Google's Colab is a free Jupyter notebook environment that requires no setup and runs entirely in the cloud. Try it out!

Useful Python libraries

Here we list several useful Python libraries we strongly recommend (if you use anaconda many of these are already there)

• NumPy is a highly popular library for large, multi-dimensional arrays and matrices, along with a large collection of high-level mathematical functions to operate on these arrays
• The pandas library provides high-performance, easy-to-use data structures and data analysis tools
• Xarray is a Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun!
• Scipy (pronounced “Sigh Pie”) is a Python-based ecosystem of open-source software for mathematics, science, and engineering.
• Matplotlib is a Python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.
• Autograd can automatically differentiate native Python and Numpy code. It can handle a large subset of Python's features, including loops, ifs, recursion and closures, and it can even take derivatives of derivatives of derivatives
• JAX has now more or less replaced Autograd. JAX is Autograd and XLA, brought together for high-performance numerical computing and machine learning research. It provides composable transformations of Python+NumPy programs: differentiate, vectorize, parallelize, Just-In-Time compile to GPU/TPU, and more.
• SymPy is a Python library for symbolic mathematics.
• scikit-learn has simple and efficient tools for machine learning, data mining and data analysis
• TensorFlow is a Python library for fast numerical computing created and released by Google
• Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano
• And many more such as pytorch, Theano etc

Installing R, C++, cython or Julia

You will also find it convenient to utilize R. We will mainly use Python during our lectures and in various projects and exercises. Those of you already familiar with R should feel free to continue using R, keeping however an eye on the parallel Python set ups. Similarly, if you are a Python afecionado, feel free to explore R as well. Jupyter(Julia, Python and R) /Ipython notebook allows you to run R codes and Julia codes interactively in your browser. The software library R is really tailored for statistical data analysis and allows for an easy usage of the tools and algorithms we will discuss in these lectures.

To install R with Jupyter notebook follow the link here

Installing R, C++, cython, Numba etc

For the C++ aficionados, Jupyter/IPython notebook allows you also to install C++ and run codes written in this language interactively in the browser. Since we will emphasize writing many of the algorithms yourself, you can thus opt for either Python or C++ (or Fortran or other compiled languages) as programming languages.

To add more entropy, cython can also be used when running your notebooks. It means that Python with the jupyter notebook setup allows you to integrate widely popular softwares and tools for scientific computing. Similarly, the Numba Python package delivers increased performance capabilities with minimal rewrites of your codes. With its versatility, including symbolic operations, Python offers a unique computational environment. Your jupyter notebook can easily be converted into a nicely rendered PDF file or a Latex file for further processing. For example, convert to latex as

pycod jupyter nbconvert filename.ipynb --to latex 

And to add more versatility, the Python package SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) and is entirely written in Python.

Finally, we recommend strongly using Autograd or JAX for automatic differentiation.

Numpy examples and Important Matrix and vector handling packages

There are several central software libraries for linear algebra and eigenvalue problems. Several of the more popular ones have been wrapped into ofter software packages like those from the widely used text Numerical Recipes. The original source codes in many of the available packages are often taken from the widely used software package LAPACK, which follows two other popular packages developed in the 1970s, namely EISPACK and LINPACK. We describe them shortly here.

• LINPACK: package for linear equations and least square problems.
• LAPACK:package for solving symmetric, unsymmetric and generalized eigenvalue problems. From LAPACK's website http://www.netlib.org it is possible to download for free all source codes from this library. Both C/C++ and Fortran versions are available.
• BLAS (I, II and III): (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. Blas I is vector operations, II vector-matrix operations and III matrix-matrix operations. Highly parallelized and efficient codes, all available for download from http://www.netlib.org.

Numpy and arrays

Numpy provides an easy way to handle arrays in Python. The standard way to import this library is as

import numpy as np

Here follows a simple example where we set up an array of ten elements, all determined by random numbers drawn according to the normal distribution,

n = 10
x = np.random.normal(size=n)
print(x)

We defined a vector $x$ with $n=10$ elements with its values given by the Normal distribution $N(0,1)$. Another alternative is to declare a vector as follows

import numpy as np
x = np.array([1, 2, 3])
print(x)

Here we have defined a vector with three elements, with $x_0=1$, $x_1=2$ and $x_2=3$. Note that both Python and C++ start numbering array elements from $0$ and on. This means that a vector with $n$ elements has a sequence of entities $x_0, x_1, x_2, \dots, x_{n-1}$. We could also let (recommended) Numpy to compute the logarithms of a specific array as

import numpy as np
x = np.log(np.array([4, 7, 8]))
print(x)

In the last example we used Numpy's unary function $np.log$. This function is highly tuned to compute array elements since the code is vectorized and does not require looping. We normaly recommend that you use the Numpy intrinsic functions instead of the corresponding log function from Python's math module. The looping is done explicitely by the np.log function. The alternative, and slower way to compute the logarithms of a vector would be to write

import numpy as np
from math import log
x = np.array([4, 7, 8])
for i in range(0, len(x)):
    x[i] = log(x[i])
print(x)

We note that our code is much longer already and we need to import the log function from the math module. The attentive reader will also notice that the output is $[1, 1, 2]$. Python interprets automagically our numbers as integers (like the automatic keyword in C++). To change this we could define our array elements to be double precision numbers as

import numpy as np
x = np.log(np.array([4, 7, 8], dtype = np.float64))
print(x)

or simply write them as double precision numbers (Python uses 64 bits as default for floating point type variables), that is

import numpy as np
x = np.log(np.array([4.0, 7.0, 8.0]))
print(x)

To check the number of bytes (remember that one byte contains eight bits for double precision variables), you can use simple use the itemsize functionality (the array $x$ is actually an object which inherits the functionalities defined in Numpy) as

import numpy as np
x = np.log(np.array([4.0, 7.0, 8.0]))
print(x.itemsize)

Matrices in Python

Having defined vectors, we are now ready to try out matrices. We can define a $3 \times 3$ real matrix $\boldsymbol{A}$ as (recall that we user lowercase letters for vectors and uppercase letters for matrices)

import numpy as np
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
print(A)

If we use the shape function we would get $(3, 3)$ as output, that is verifying that our matrix is a $3\times 3$ matrix. We can slice the matrix and print for example the first column (Python organized matrix elements in a row-major order, see below) as

import numpy as np
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
# print the first column, row-major order and elements start with 0
print(A[:,0]) 

We can continue this was by printing out other columns or rows. The example here prints out the second column

import numpy as np
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
# print the first column, row-major order and elements start with 0
print(A[1,:]) 

Numpy contains many other functionalities that allow us to slice, subdivide etc etc arrays. We strongly recommend that you look up the Numpy website for more details. Useful functions when defining a matrix are the np.zeros function which declares a matrix of a given dimension and sets all elements to zero

import numpy as np
n = 10
# define a matrix of dimension 10 x 10 and set all elements to zero
A = np.zeros( (n, n) )
print(A) 

or initializing all elements to

import numpy as np
n = 10
# define a matrix of dimension 10 x 10 and set all elements to one
A = np.ones( (n, n) )
print(A) 

or as unitarily distributed random numbers (see the material on random number generators in the statistics part)

import numpy as np
n = 10
# define a matrix of dimension 10 x 10 and set all elements to random numbers with x \in [0, 1]
A = np.random.rand(n, n)
print(A) 

As we will see throughout these lectures, there are several extremely useful functionalities in Numpy. As an example, consider the discussion of the covariance matrix. Suppose we have defined three vectors $\boldsymbol{x}, \boldsymbol{y}, \boldsymbol{z}$ with $n$ elements each. The covariance matrix is defined as

 
$$\boldsymbol{\Sigma} = \begin{bmatrix} \sigma_{xx} & \sigma_{xy} & \sigma_{xz} \\ \sigma_{yx} & \sigma_{yy} & \sigma_{yz} \\ \sigma_{zx} & \sigma_{zy} & \sigma_{zz} \end{bmatrix},$$

where for example

 
$$\sigma_{xy} =\frac{1}{n} \sum_{i=0}^{n-1}(x_i- \overline{x})(y_i- \overline{y}).$$

The Numpy function np.cov calculates the covariance elements using the factor $1/(n-1)$ instead of $1/n$ since it assumes we do not have the exact mean values. The following simple function uses the np.vstack function which takes each vector of dimension $1\times n$ and produces a $3\times n$ matrix $\boldsymbol{W}$

 
$$\boldsymbol{W} = \begin{bmatrix} x_0 & x_1 & x_2 & \dots & x_{n-2} & x_{n-1} \\ y_0 & y_1 & y_2 & \dots & y_{n-2} & y_{n-1} \\ z_0 & z_1 & z_2 & \dots & z_{n-2} & z_{n-1} \\ \end{bmatrix},$$

which in turn is converted into into the $3\times 3$ covariance matrix $\boldsymbol{\Sigma}$ via the Numpy function np.cov(). We note that we can also calculate the mean value of each set of samples $\boldsymbol{x}$ etc using the Numpy function np.mean(x). We can also extract the eigenvalues of the covariance matrix through the np.linalg.eig() function.

# Importing various packages
import numpy as np

n = 100
x = np.random.normal(size=n)
print(np.mean(x))
y = 4+3*x+np.random.normal(size=n)
print(np.mean(y))
z = x**3+np.random.normal(size=n)
print(np.mean(z))
W = np.vstack((x, y, z))
Sigma = np.cov(W)
print(Sigma)
Eigvals, Eigvecs = np.linalg.eig(Sigma)
print(Eigvals)

import numpy as np
import matplotlib.pyplot as plt
from scipy import sparse
eye = np.eye(4)
print(eye)
sparse_mtx = sparse.csr_matrix(eye)
print(sparse_mtx)
x = np.linspace(-10,10,100)
y = np.sin(x)
plt.plot(x,y,marker='x')
plt.show()

Meet the Pandas

Another useful Python package is pandas, which is an open source library providing high-performance, easy-to-use data structures and data analysis tools for Python. pandas stands for panel data, a term borrowed from econometrics and is an efficient library for data analysis with an emphasis on tabular data. pandas has two major classes, the DataFrame class with two-dimensional data objects and tabular data organized in columns and the class Series with a focus on one-dimensional data objects. Both classes allow you to index data easily as we will see in the examples below. pandas allows you also to perform mathematical operations on the data, spanning from simple reshapings of vectors and matrices to statistical operations.

The following simple example shows how we can, in an easy way make tables of our data. Here we define a data set which includes names, place of birth and date of birth, and displays the data in an easy to read way. We will see repeated use of pandas, in particular in connection with classification of data.

import pandas as pd
from IPython.display import display
data = {'First Name': ["Frodo", "Bilbo", "Aragorn II", "Samwise"],
        'Last Name': ["Baggins", "Baggins","Elessar","Gamgee"],
        'Place of birth': ["Shire", "Shire", "Eriador", "Shire"],
        'Date of Birth T.A.': [2968, 2890, 2931, 2980]
        }
data_pandas = pd.DataFrame(data)
display(data_pandas)

In the above we have imported pandas with the shorthand pd, the latter has become the standard way we import pandas. We make then a list of various variables and reorganize the aboves lists into a DataFrame and then print out a neat table with specific column labels as Name, place of birth and date of birth. Displaying these results, we see that the indices are given by the default numbers from zero to three. pandas is extremely flexible and we can easily change the above indices by defining a new type of indexing as

data_pandas = pd.DataFrame(data,index=['Frodo','Bilbo','Aragorn','Sam'])
display(data_pandas)

Thereafter we display the content of the row which begins with the index Aragorn

display(data_pandas.loc['Aragorn'])

We can easily append data to this, for example

new_hobbit = {'First Name': ["Peregrin"],
              'Last Name': ["Took"],
              'Place of birth': ["Shire"],
              'Date of Birth T.A.': [2990]
              }
data_pandas=data_pandas.append(pd.DataFrame(new_hobbit, index=['Pippin']))
display(data_pandas)

Here are other examples where we use the DataFrame functionality to handle arrays, now with more interesting features for us, namely numbers. We set up a matrix of dimensionality $10\times 5$ and compute the mean value and standard deviation of each column. Similarly, we can perform mathematial operations like squaring the matrix elements and many other operations.

import numpy as np
import pandas as pd
from IPython.display import display
np.random.seed(100)
# setting up a 10 x 5 matrix
rows = 10
cols = 5
a = np.random.randn(rows,cols)
df = pd.DataFrame(a)
display(df)
print(df.mean())
print(df.std())
display(df**2)

Thereafter we can select specific columns only and plot final results

df.columns = ['First', 'Second', 'Third', 'Fourth', 'Fifth']
df.index = np.arange(10)

display(df)
print(df['Second'].mean() )
print(df.info())
print(df.describe())

from pylab import plt, mpl
plt.style.use('seaborn')
mpl.rcParams['font.family'] = 'serif'

df.cumsum().plot(lw=2.0, figsize=(10,6))
plt.show()


df.plot.bar(figsize=(10,6), rot=15)
plt.show()

We can produce a $4\times 4$ matrix

b = np.arange(16).reshape((4,4))
print(b)
df1 = pd.DataFrame(b)
print(df1)

and many other operations.

The Series class is another important class included in pandas. You can view it as a specialization of DataFrame but where we have just a single column of data. It shares many of the same features as DataFrame. As with DataFrame, most operations are vectorized, achieving thereby a high performance when dealing with computations of arrays, in particular labeled arrays. As we will see below it leads also to a very concice code close to the mathematical operations we may be interested in. For multidimensional arrays, we recommend strongly xarray. xarray has much of the same flexibility as pandas, but allows for the extension to higher dimensions than two. We will see examples later of the usage of both pandas and xarray.

Simple linear regression model using scikit-learn

We start with perhaps our simplest possible example, using Scikit-Learn to perform linear regression analysis on a data set produced by us.

What follows is a simple Python code where we have defined a function $y$ in terms of the variable $x$. Both are defined as vectors with $100$ entries. The numbers in the vector $\boldsymbol{x}$ are given by random numbers generated with a uniform distribution with entries $x_i \in [0,1]$ (more about probability distribution functions later). These values are then used to define a function $y(x)$ (tabulated again as a vector) with a linear dependence on $x$ plus a random noise added via the normal distribution.

The Numpy functions are imported used the import numpy as np statement and the random number generator for the uniform distribution is called using the function np.random.rand(), where we specificy that we want $100$ random variables. Using Numpy we define automatically an array with the specified number of elements, $100$ in our case. With the Numpy function randn() we can compute random numbers with the normal distribution (mean value $\mu$ equal to zero and variance $\sigma^2$ set to one) and produce the values of $y$ assuming a linear dependence as function of $x$

 
$$y = 2x+N(0,1),$$

where $N(0,1)$ represents random numbers generated by the normal distribution. From Scikit-Learn we import then the LinearRegression functionality and make a prediction $\tilde{y} = \alpha + \beta x$ using the function fit(x,y). We call the set of data $(\boldsymbol{x},\boldsymbol{y})$ for our training data. The Python package scikit-learn has also a functionality which extracts the above fitting parameters $\alpha$ and $\beta$ (see below). Later we will distinguish between training data and test data.

For plotting we use the Python package matplotlib which produces publication quality figures. Feel free to explore the extensive gallery of examples. In this example we plot our original values of $x$ and $y$ as well as the prediction ypredict ($\tilde{y}$), which attempts at fitting our data with a straight line.

The Python code follows here.

# Importing various packages
import numpy as np
import matplotlib.pyplot as plt
from sklearn.linear_model import LinearRegression

x = np.random.rand(100,1)
y = 2*x+np.random.randn(100,1)
linreg = LinearRegression()
linreg.fit(x,y)
xnew = np.array([[0],[1]])
ypredict = linreg.predict(xnew)

plt.plot(xnew, ypredict, "r-")
plt.plot(x, y ,'ro')
plt.axis([0,1.0,0, 5.0])
plt.xlabel(r'$x$')
plt.ylabel(r'$y$')
plt.title(r'Simple Linear Regression')
plt.show()

This example serves several aims. It allows us to demonstrate several aspects of data analysis and later machine learning algorithms. The immediate visualization shows that our linear fit is not impressive. It goes through the data points, but there are many outliers which are not reproduced by our linear regression. We could now play around with this small program and change for example the factor in front of $x$ and the normal distribution. Try to change the function $y$ to

 
$$y = 10x+0.01 \times N(0,1),$$

where $x$ is defined as before. Does the fit look better? Indeed, by reducing the role of the noise given by the normal distribution we see immediately that our linear prediction seemingly reproduces better the training set. However, this testing 'by the eye' is obviouly not satisfactory in the long run. Here we have only defined the training data and our model, and have not discussed a more rigorous approach to the cost function.

We need more rigorous criteria in defining whether we have succeeded or not in modeling our training data. You will be surprised to see that many scientists seldomly venture beyond this 'by the eye' approach. A standard approach for the cost function is the so-called $\chi^2$ function (a variant of the mean-squared error (MSE))

 
$$\chi^2 = \frac{1}{n} \sum_{i=0}^{n-1}\frac{(y_i-\tilde{y}_i)^2}{\sigma_i^2},$$

where $\sigma_i^2$ is the variance (to be defined later) of the entry $y_i$. We may not know the explicit value of $\sigma_i^2$, it serves however the aim of scaling the equations and make the cost function dimensionless.

Minimizing the cost function is a central aspect of our discussions to come. Finding its minima as function of the model parameters ($\alpha$ and $\beta$ in our case) will be a recurring theme in these series of lectures. Essentially all machine learning algorithms we will discuss center around the minimization of the chosen cost function. This depends in turn on our specific model for describing the data, a typical situation in supervised learning. Automatizing the search for the minima of the cost function is a central ingredient in all algorithms. Typical methods which are employed are various variants of gradient methods. These will be discussed in more detail later. Again, you'll be surprised to hear that many practitioners minimize the above function ''by the eye', popularly dubbed as 'chi by the eye'. That is, change a parameter and see (visually and numerically) that the $\chi^2$ function becomes smaller.

There are many ways to define the cost function. A simpler approach is to look at the relative difference between the training data and the predicted data, that is we define the relative error (why would we prefer the MSE instead of the relative error?) as

 
$$\epsilon_{\mathrm{relative}}= \frac{\vert \boldsymbol{y} -\boldsymbol{\tilde{y}}\vert}{\vert \boldsymbol{y}\vert}.$$

The squared cost function results in an arithmetic mean-unbiased estimator, and the absolute-value cost function results in a median-unbiased estimator (in the one-dimensional case, and a geometric median-unbiased estimator for the multi-dimensional case). The squared cost function has the disadvantage that it has the tendency to be dominated by outliers.

We can modify easily the above Python code and plot the relative error instead

import numpy as np
import matplotlib.pyplot as plt
from sklearn.linear_model import LinearRegression

x = np.random.rand(100,1)
y = 5*x+0.01*np.random.randn(100,1)
linreg = LinearRegression()
linreg.fit(x,y)
ypredict = linreg.predict(x)

plt.plot(x, np.abs(ypredict-y)/abs(y), "ro")
plt.axis([0,1.0,0.0, 0.5])
plt.xlabel(r'$x$')
plt.ylabel(r'$\epsilon_{\mathrm{relative}}$')
plt.title(r'Relative error')
plt.show()

Depending on the parameter in front of the normal distribution, we may have a small or larger relative error. Try to play around with different training data sets and study (graphically) the value of the relative error.

As mentioned above, Scikit-Learn has an impressive functionality. We can for example extract the values of $\alpha$ and $\beta$ and their error estimates, or the variance and standard deviation and many other properties from the statistical data analysis.

Here we show an example of the functionality of Scikit-Learn.

import numpy as np 
import matplotlib.pyplot as plt 
from sklearn.linear_model import LinearRegression 
from sklearn.metrics import mean_squared_error, r2_score, mean_squared_log_error, mean_absolute_error

x = np.random.rand(100,1)
y = 2.0+ 5*x+0.5*np.random.randn(100,1)
linreg = LinearRegression()
linreg.fit(x,y)
ypredict = linreg.predict(x)
print('The intercept alpha: \n', linreg.intercept_)
print('Coefficient beta : \n', linreg.coef_)
# The mean squared error                               
print("Mean squared error: %.2f" % mean_squared_error(y, ypredict))
# Explained variance score: 1 is perfect prediction                                 
print('Variance score: %.2f' % r2_score(y, ypredict))
# Mean squared log error                                                        
print('Mean squared log error: %.2f' % mean_squared_log_error(y, ypredict) )
# Mean absolute error                                                           
print('Mean absolute error: %.2f' % mean_absolute_error(y, ypredict))
plt.plot(x, ypredict, "r-")
plt.plot(x, y ,'ro')
plt.axis([0.0,1.0,1.5, 7.0])
plt.xlabel(r'$x$')
plt.ylabel(r'$y$')
plt.title(r'Linear Regression fit ')
plt.show()

The function coef gives us the parameter $\beta$ of our fit while intercept yields $\alpha$. Depending on the constant in front of the normal distribution, we get values near or far from $\alpha =2$ and $\beta =5$. Try to play around with different parameters in front of the normal distribution. The function meansquarederror gives us the mean square error, a risk metric corresponding to the expected value of the squared (quadratic) error or loss defined as

 
$$MSE(\boldsymbol{y},\boldsymbol{\tilde{y}}) = \frac{1}{n} \sum_{i=0}^{n-1}(y_i-\tilde{y}_i)^2,$$

The smaller the value, the better the fit. Ideally we would like to have an MSE equal zero. The attentive reader has probably recognized this function as being similar to the $\chi^2$ function defined above.

The r2score function computes $R^2$, the coefficient of determination. It provides a measure of how well future samples are likely to be predicted by the model. Best possible score is 1.0 and it can be negative (because the model can be arbitrarily worse). A constant model that always predicts the expected value of $\boldsymbol{y}$, disregarding the input features, would get a $R^2$ score of $0.0$.

If $\tilde{\boldsymbol{y}}_i$ is the predicted value of the $i-th$ sample and $y_i$ is the corresponding true value, then the score $R^2$ is defined as

 
$$R^2(\boldsymbol{y}, \tilde{\boldsymbol{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i - \tilde{y}_i)^2}{\sum_{i=0}^{n - 1} (y_i - \bar{y})^2},$$

where we have defined the mean value of $\boldsymbol{y}$ as

 
$$\bar{y} = \frac{1}{n} \sum_{i=0}^{n - 1} y_i.$$

Another quantity taht we will meet again in our discussions of regression analysis is the mean absolute error (MAE), a risk metric corresponding to the expected value of the absolute error loss or what we call the $l1$-norm loss. In our discussion above we presented the relative error. The MAE is defined as follows

 
$$\text{MAE}(\boldsymbol{y}, \boldsymbol{\tilde{y}}) = \frac{1}{n} \sum_{i=0}^{n-1} \left| y_i - \tilde{y}_i \right|.$$

We present the squared logarithmic (quadratic) error

 
$$\text{MSLE}(\boldsymbol{y}, \boldsymbol{\tilde{y}}) = \frac{1}{n} \sum_{i=0}^{n - 1} (\log_e (1 + y_i) - \log_e (1 + \tilde{y}_i) )^2,$$

where $\log_e (x)$ stands for the natural logarithm of $x$. This error estimate is best to use when targets having exponential growth, such as population counts, average sales of a commodity over a span of years etc.

Finally, another cost function is the Huber cost function used in robust regression.

The rationale behind this possible cost function is its reduced sensitivity to outliers in the data set. In our discussions on dimensionality reduction and normalization of data we will meet other ways of dealing with outliers.

The Huber cost function is defined as

 
$$H_{\delta}(\boldsymbol{a})=\left\{\begin{array}{cc}\frac{1}{2} \boldsymbol{a}^{2}& \text{for }|\boldsymbol{a}|\leq \delta\\ \delta (|\boldsymbol{a}|-\frac{1}{2}\delta ),&\text{otherwise}.\end{array}\right.$$

Here $\boldsymbol{a}=\boldsymbol{y} - \boldsymbol{\tilde{y}}$.

We will discuss in more detail these and other functions in the various lectures and lab sessions.

To our real data: nuclear binding energies. Brief reminder on masses and binding energies

Let us now dive into nuclear physics and remind ourselves briefly about some basic features about binding energies. A basic quantity which can be measured for the ground states of nuclei is the atomic mass $M(N, Z)$ of the neutral atom with atomic mass number $A$ and charge $Z$. The number of neutrons is $N$. There are indeed several sophisticated experiments worldwide which allow us to measure this quantity to high precision (parts per million even).

Atomic masses are usually tabulated in terms of the mass excess defined by

 
$$\Delta M(N, Z) = M(N, Z) - uA,$$

where $u$ is the Atomic Mass Unit

 
$$u = M(^{12}\mathrm{C})/12 = 931.4940954(57) \hspace{0.1cm} \mathrm{MeV}/c^2.$$

The nucleon masses are

 
$$m_p = 1.00727646693(9)u,$$

and

 
$$m_n = 939.56536(8)\hspace{0.1cm} \mathrm{MeV}/c^2 = 1.0086649156(6)u.$$

In the 2016 mass evaluation of by W.J.Huang, G.Audi, M.Wang, F.G.Kondev, S.Naimi and X.Xu there are data on masses and decays of 3437 nuclei.

The nuclear binding energy is defined as the energy required to break up a given nucleus into its constituent parts of $N$ neutrons and $Z$ protons. In terms of the atomic masses $M(N, Z)$ the binding energy is defined by

 
$$BE(N, Z) = ZM_H c^2 + Nm_n c^2 - M(N, Z)c^2 ,$$

where $M_H$ is the mass of the hydrogen atom and $m_n$ is the mass of the neutron. In terms of the mass excess the binding energy is given by

 
$$BE(N, Z) = Z\Delta_H c^2 + N\Delta_n c^2 -\Delta(N, Z)c^2 ,$$

where $\Delta_H c^2 = 7.2890$ MeV and $\Delta_n c^2 = 8.0713$ MeV.

A popular and physically intuitive model which can be used to parametrize the experimental binding energies as function of $A$, is the so-called liquid drop model. The ansatz is based on the following expression

 
$$BE(N,Z) = a_1A-a_2A^{2/3}-a_3\frac{Z^2}{A^{1/3}}-a_4\frac{(N-Z)^2}{A},$$

where $A$ stands for the number of nucleons and the $a_i$s are parameters which are determined by a fit to the experimental data.

To arrive at the above expression we have assumed that we can make the following assumptions:

• There is a volume term $a_1A$ proportional with the number of nucleons (the energy is also an extensive quantity). When an assembly of nucleons of the same size is packed together into the smallest volume, each interior nucleon has a certain number of other nucleons in contact with it. This contribution is proportional to the volume.
• There is a surface energy term $a_2A^{2/3}$. The assumption here is that a nucleon at the surface of a nucleus interacts with fewer other nucleons than one in the interior of the nucleus and hence its binding energy is less. This surface energy term takes that into account and is therefore negative and is proportional to the surface area.
• There is a Coulomb energy term $a_3\frac{Z^2}{A^{1/3}}$. The electric repulsion between each pair of protons in a nucleus yields less binding.
• There is an asymmetry term $a_4\frac{(N-Z)^2}{A}$. This term is associated with the Pauli exclusion principle and reflects the fact that the proton-neutron interaction is more attractive on the average than the neutron-neutron and proton-proton interactions.

We could also add a so-called pairing term, which is a correction term that arises from the tendency of proton pairs and neutron pairs to occur. An even number of particles is more stable than an odd number.

Organizing our data

Let us start with reading and organizing our data. We start with the compilation of masses and binding energies from 2016. After having downloaded this file to our own computer, we are now ready to read the file and start structuring our data.

We start with preparing folders for storing our calculations and the data file over masses and binding energies. We import also various modules that we will find useful in order to present various Machine Learning methods. Here we focus mainly on the functionality of scikit-learn.

# Common imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sklearn.linear_model as skl
from sklearn.model_selection import train_test_split
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_error
import os

# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

infile = open(data_path("MassEval2016.dat"),'r')

Before we proceed, we define also a function for making our plots. You can obviously avoid this and simply set up various matplotlib commands every time you need them. You may however find it convenient to collect all such commands in one function and simply call this function.

from pylab import plt, mpl
plt.style.use('seaborn')
mpl.rcParams['font.family'] = 'serif'

def MakePlot(x,y, styles, labels, axlabels):
    plt.figure(figsize=(10,6))
    for i in range(len(x)):
        plt.plot(x[i], y[i], styles[i], label = labels[i])
        plt.xlabel(axlabels[0])
        plt.ylabel(axlabels[1])
    plt.legend(loc=0)

Our next step is to read the data on experimental binding energies and reorganize them as functions of the mass number $A$, the number of protons $Z$ and neutrons $N$ using pandas. Before we do this it is always useful (unless you have a binary file or other types of compressed data) to actually open the file and simply take a look at it!

In particular, the program that outputs the final nuclear masses is written in Fortran with a specific format. It means that we need to figure out the format and which columns contain the data we are interested in. Pandas comes with a function that reads formatted output. After having admired the file, we are now ready to start massaging it with pandas. The file begins with some basic format information.

"""                                                                                                                         
This is taken from the data file of the mass 2016 evaluation.                                                               
All files are 3436 lines long with 124 character per line.                                                                  
       Headers are 39 lines long.                                                                                           
   col 1     :  Fortran character control: 1 = page feed  0 = line feed                                                     
   format    :  a1,i3,i5,i5,i5,1x,a3,a4,1x,f13.5,f11.5,f11.3,f9.3,1x,a2,f11.3,f9.3,1x,i3,1x,f12.5,f11.5                     
   These formats are reflected in the pandas widths variable below, see the statement                                       
   widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),                                                            
   Pandas has also a variable header, with length 39 in this case.                                                          
"""

The data we are interested in are in columns 2, 3, 4 and 11, giving us the number of neutrons, protons, mass numbers and binding energies, respectively. We add also for the sake of completeness the element name. The data are in fixed-width formatted lines and we will covert them into the pandas DataFrame structure.

# Read the experimental data with Pandas
Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
              header=39,
              index_col=False)

# Extrapolated values are indicated by '#' in place of the decimal place, so
# the Ebinding column won't be numeric. Coerce to float and drop these entries.
Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
Masses = Masses.dropna()
# Convert from keV to MeV.
Masses['Ebinding'] /= 1000

# Group the DataFrame by nucleon number, A.
Masses = Masses.groupby('A')
# Find the rows of the grouped DataFrame with the maximum binding energy.
Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])

We have now read in the data, grouped them according to the variables we are interested in. We see how easy it is to reorganize the data using pandas. If we were to do these operations in C/C++ or Fortran, we would have had to write various functions/subroutines which perform the above reorganizations for us. Having reorganized the data, we can now start to make some simple fits using both the functionalities in numpy and Scikit-Learn afterwards.

Now we define five variables which contain the number of nucleons $A$, the number of protons $Z$ and the number of neutrons $N$, the element name and finally the energies themselves.

A = Masses['A']
Z = Masses['Z']
N = Masses['N']
Element = Masses['Element']
Energies = Masses['Ebinding']
print(Masses)

The next step, and we will define this mathematically later, is to set up the so-called design matrix. We will throughout call this matrix $\boldsymbol{X}$. It has dimensionality $p\times n$, where $n$ is the number of data points and $p$ are the so-called predictors. In our case here they are given by the number of polynomials in $A$ we wish to include in the fit.

# Now we set up the design matrix X
X = np.zeros((len(A),5))
X[:,0] = 1
X[:,1] = A
X[:,2] = A**(2.0/3.0)
X[:,3] = A**(-1.0/3.0)
X[:,4] = A**(-1.0)

With scikitlearn we are now ready to use linear regression and fit our data.

clf = skl.LinearRegression().fit(X, Energies)
fity = clf.predict(X)

Pretty simple! Now we can print measures of how our fit is doing, the coefficients from the fits and plot the final fit together with our data.

# The mean squared error                               
print("Mean squared error: %.2f" % mean_squared_error(Energies, fity))
# Explained variance score: 1 is perfect prediction                                 
print('Variance score: %.2f' % r2_score(Energies, fity))
# Mean absolute error                                                           
print('Mean absolute error: %.2f' % mean_absolute_error(Energies, fity))
print(clf.coef_, clf.intercept_)

Masses['Eapprox']  = fity
# Generate a plot comparing the experimental with the fitted values values.
fig, ax = plt.subplots()
ax.set_xlabel(r'$A = N + Z$')
ax.set_ylabel(r'$E_\mathrm{bind}\,/\mathrm{MeV}$')
ax.plot(Masses['A'], Masses['Ebinding'], alpha=0.7, lw=2,
            label='Ame2016')
ax.plot(Masses['A'], Masses['Eapprox'], alpha=0.7, lw=2, c='m',
            label='Fit')
ax.legend()
save_fig("Masses2016")
plt.show()

And what about using neural networks?

The seaborn package allows us to visualize data in an efficient way. Note that we use scikit-learn's multi-layer perceptron (or feed forward neural network) functionality.

from sklearn.neural_network import MLPRegressor
from sklearn.metrics import accuracy_score
import seaborn as sns

X_train = X
Y_train = Energies
n_hidden_neurons = 100
epochs = 100
# store models for later use
eta_vals = np.logspace(-5, 1, 7)
lmbd_vals = np.logspace(-5, 1, 7)
# store the models for later use
DNN_scikit = np.zeros((len(eta_vals), len(lmbd_vals)), dtype=object)
train_accuracy = np.zeros((len(eta_vals), len(lmbd_vals)))
sns.set()
for i, eta in enumerate(eta_vals):
    for j, lmbd in enumerate(lmbd_vals):
        dnn = MLPRegressor(hidden_layer_sizes=(n_hidden_neurons), activation='logistic',
                            alpha=lmbd, learning_rate_init=eta, max_iter=epochs)
        dnn.fit(X_train, Y_train)
        DNN_scikit[i][j] = dnn
        train_accuracy[i][j] = dnn.score(X_train, Y_train)

fig, ax = plt.subplots(figsize = (10, 10))
sns.heatmap(train_accuracy, annot=True, ax=ax, cmap="viridis")
ax.set_title("Training Accuracy")
ax.set_ylabel("$\eta$")
ax.set_xlabel("$\lambda$")
plt.show()

More on flexibility with pandas and xarray

Let us study the $Q$ values associated with the removal of one or two nucleons from a nucleus. These are conventionally defined in terms of the one-nucleon and two-nucleon separation energies. With the functionality in pandas, two to three lines of code will allow us to plot the separation energies. The neutron separation energy is defined as

 
$$S_n= -Q_n= BE(N,Z)-BE(N-1,Z),$$

and the proton separation energy reads

 
$$S_p= -Q_p= BE(N,Z)-BE(N,Z-1).$$

The two-neutron separation energy is defined as

 
$$S_{2n}= -Q_{2n}= BE(N,Z)-BE(N-2,Z),$$

and the two-proton separation energy is given by

 
$$S_{2p}= -Q_{2p}= BE(N,Z)-BE(N,Z-2).$$

Using say the neutron separation energies (alternatively the proton separation energies)

 
$$S_n= -Q_n= BE(N,Z)-BE(N-1,Z),$$

we can define the so-called energy gap for neutrons (or protons) as

 
$$\Delta S_n= BE(N,Z)-BE(N-1,Z)-\left(BE(N+1,Z)-BE(N,Z)\right),$$

or

 
$$\Delta S_n= 2BE(N,Z)-BE(N-1,Z)-BE(N+1,Z).$$

This quantity can in turn be used to determine which nuclei could be interpreted as magic or not. For protons we would have

 
$$\Delta S_p= 2BE(N,Z)-BE(N,Z-1)-BE(N,Z+1).$$

To calculate say the neutron separation we need to multiply our masses with the nucleon number $A$ (why?). Thereafter we pick the oxygen isotopes and simply compute the separation energies with two lines of code (note that most of the code here is a repeat of what you have seen before).

# Common imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
from pylab import plt, mpl
plt.style.use('seaborn')
mpl.rcParams['font.family'] = 'serif'

def MakePlot(x,y, styles, labels, axlabels):
    plt.figure(figsize=(10,6))
    for i in range(len(x)):
        plt.plot(x[i], y[i], styles[i], label = labels[i])
        plt.xlabel(axlabels[0])
        plt.ylabel(axlabels[1])
    plt.legend(loc=0)



# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

infile = open(data_path("MassEval2016.dat"),'r')


# Read the experimental data with Pandas
Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
              header=39,
              index_col=False)

# Extrapolated values are indicated by '#' in place of the decimal place, so
# the Ebinding column won't be numeric. Coerce to float and drop these entries.
Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
Masses = Masses.dropna()
# Convert from keV to MeV.
Masses['Ebinding'] /= 1000
A = Masses['A']
Z = Masses['Z']
N = Masses['N']
Element = Masses['Element']
Energies = Masses['Ebinding']*A

df = pd.DataFrame({'A':A,'Z':Z, 'N':N,'Element':Element,'Energies':Energies})
# Her we pick the oyxgen isotopes
Nucleus = df.loc[lambda df: df.Z==8, :]
# drop cases with no number
Nucleus = Nucleus.dropna()
# Here we do the magic and obtain the neutron separation energies, one line of code!!
Nucleus['NeutronSeparationEnergies'] = Nucleus['Energies'].diff(+1)
print(Nucleus)
MakePlot([Nucleus.A], [Nucleus.NeutronSeparationEnergies], ['b'], ['Neutron Separation Energy'], ['$A$','$S_n$'])
save_fig('Nucleus')
plt.show()

A first summary

The aim behind these introductory words was to present to you various Python libraries and their functionalities, in particular libraries like numpy, pandas, xarray and matplotlib and other that make our life much easier in handling various data sets and visualizing data.

Furthermore, Scikit-Learn allows us with few lines of code to implement popular Machine Learning algorithms for supervised learning. Later we will meet Tensorflow, a powerful library for deep learning. Now it is time to dive more into the details of various methods. We will start with linear regression and try to take a deeper look at what it entails.

Why Linear Regression (aka Ordinary Least Squares and family)

Fitting a continuous function with linear parameterization in terms of the parameters $\boldsymbol{\beta}$.

• Method of choice for fitting a continuous function!
• Gives an excellent introduction to central Machine Learning features with understandable pedagogical links to other methods like Neural Networks, Support Vector Machines etc
• Analytical expression for the fitting parameters $\boldsymbol{\beta}$
• Analytical expressions for statistical propertiers like mean values, variances, confidence intervals and more
• Analytical relation with probabilistic interpretations
• Easy to introduce basic concepts like bias-variance tradeoff, cross-validation, resampling and regularization techniques and many other ML topics
• Easy to code! And links well with classification problems and logistic regression and neural networks
• Allows for easy hands-on understanding of gradient descent methods
• and many more features

For more discussions of Ridge and Lasso regression, Wessel van Wieringen's article is highly recommended. Similarly, Mehta et al's article is also recommended.

Regression analysis, overarching aims

Regression analysis, overarching aims II

Examples

General linear models and linear algebra

Rewriting the fitting procedure as a linear algebra problem

Rewriting the fitting procedure as a linear algebra problem, more details

Generalizing the fitting procedure as a linear algebra problem

Generalizing the fitting procedure as a linear algebra problem

Optimizing our parameters

Our model for the nuclear binding energies

In our introductory notes we looked at the so-called liquid drop model. Let us remind ourselves about what we did by looking at the code.

We restate the parts of the code we are most interested in.

# Common imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from IPython.display import display
import os

# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

infile = open(data_path("MassEval2016.dat"),'r')


# Read the experimental data with Pandas
Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
              header=39,
              index_col=False)

# Extrapolated values are indicated by '#' in place of the decimal place, so
# the Ebinding column won't be numeric. Coerce to float and drop these entries.
Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
Masses = Masses.dropna()
# Convert from keV to MeV.
Masses['Ebinding'] /= 1000

# Group the DataFrame by nucleon number, A.
Masses = Masses.groupby('A')
# Find the rows of the grouped DataFrame with the maximum binding energy.
Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])
A = Masses['A']
Z = Masses['Z']
N = Masses['N']
Element = Masses['Element']
Energies = Masses['Ebinding']

# Now we set up the design matrix X
X = np.zeros((len(A),5))
X[:,0] = 1
X[:,1] = A
X[:,2] = A**(2.0/3.0)
X[:,3] = A**(-1.0/3.0)
X[:,4] = A**(-1.0)
# Then nice printout using pandas
DesignMatrix = pd.DataFrame(X)
DesignMatrix.index = A
DesignMatrix.columns = ['1', 'A', 'A^(2/3)', 'A^(-1/3)', '1/A']
display(DesignMatrix)

With $\boldsymbol{\beta}\in {\mathbb{R}}^{p\times 1}$, it means that we will hereafter write our equations for the approximation as

 
$$\boldsymbol{\tilde{y}}= \boldsymbol{X}\boldsymbol{\beta},$$

throughout these lectures.

Optimizing our parameters, more details

Interpretations and optimizing our parameters

Interpretations and optimizing our parameters

Some useful matrix and vector expressions

See the handwritten notes at https://github.com/CompPhysics/MachineLearning/blob/master/doc/HandWrittenNotes/2022/NotesExercise5Week452022.pdf

These notes will be discussed during one of the lectures.

Interpretations and optimizing our parameters

Let us now return to our nuclear binding energies and simply code the above equations.

Own code for Ordinary Least Squares

It is rather straightforward to implement the matrix inversion and obtain the parameters $\boldsymbol{\beta}$. After having defined the matrix $\boldsymbol{X}$ we simply need to write

# matrix inversion to find beta
beta = np.linalg.inv(X.T.dot(X)).dot(X.T).dot(Energies)
# and then make the prediction
ytilde = X @ beta

Alternatively, you can use the least squares functionality in Numpy as

fit = np.linalg.lstsq(X, Energies, rcond =None)[0]
ytildenp = np.dot(fit,X.T)

And finally we plot our fit with and compare with data

Masses['Eapprox']  = ytilde
# Generate a plot comparing the experimental with the fitted values values.
fig, ax = plt.subplots()
ax.set_xlabel(r'$A = N + Z$')
ax.set_ylabel(r'$E_\mathrm{bind}\,/\mathrm{MeV}$')
ax.plot(Masses['A'], Masses['Ebinding'], alpha=0.7, lw=2,
            label='Ame2016')
ax.plot(Masses['A'], Masses['Eapprox'], alpha=0.7, lw=2, c='m',
            label='Fit')
ax.legend()
save_fig("Masses2016OLS")
plt.show()

Adding error analysis and training set up

We can easily test our fit by computing the $R2$ score that we discussed in connection with the functionality of Scikit-Learn in the introductory slides. Since we are not using Scikit-Learn here we can define our own $R2$ function as

def R2(y_data, y_model):
    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)

and we would be using it as

print(R2(Energies,ytilde))

We can easily add our MSE score as

def MSE(y_data,y_model):
    n = np.size(y_model)
    return np.sum((y_data-y_model)**2)/n

print(MSE(Energies,ytilde))

and finally the relative error as

def RelativeError(y_data,y_model):
    return abs((y_data-y_model)/y_data)
print(RelativeError(Energies, ytilde))

The $\chi^2$ function

The $\chi^2$ function

The $\chi^2$ function

The $\chi^2$ function

The $\chi^2$ function

The $\chi^2$ function

Fitting an Equation of State for Dense Nuclear Matter

Before we continue, let us introduce yet another example. We are going to fit the nuclear equation of state using results from many-body calculations. The equation of state we have made available here, as function of density, has been derived using modern nucleon-nucleon potentials with the addition of three-body forces. This time the file is presented as a standard csv file.

The beginning of the Python code here is similar to what you have seen before, with the same initializations and declarations. We use also pandas again, rather extensively in order to organize our data.

The difference now is that we use Scikit-Learn's regression tools instead of our own matrix inversion implementation. Furthermore, we sneak in Ridge regression (to be discussed below) which includes a hyperparameter $\lambda$, also to be explained below.

The code

# Common imports
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.pyplot as plt
import sklearn.linear_model as skl
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_error

# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

infile = open(data_path("EoS.csv"),'r')

# Read the EoS data as  csv file and organize the data into two arrays with density and energies
EoS = pd.read_csv(infile, names=('Density', 'Energy'))
EoS['Energy'] = pd.to_numeric(EoS['Energy'], errors='coerce')
EoS = EoS.dropna()
Energies = EoS['Energy']
Density = EoS['Density']
#  The design matrix now as function of various polytrops
X = np.zeros((len(Density),4))
X[:,3] = Density**(4.0/3.0)
X[:,2] = Density
X[:,1] = Density**(2.0/3.0)
X[:,0] = 1

# We use now Scikit-Learn's linear regressor and ridge regressor
# OLS part
clf = skl.LinearRegression().fit(X, Energies)
ytilde = clf.predict(X)
EoS['Eols']  = ytilde
# The mean squared error                               
print("Mean squared error: %.2f" % mean_squared_error(Energies, ytilde))
# Explained variance score: 1 is perfect prediction                                 
print('Variance score: %.2f' % r2_score(Energies, ytilde))
# Mean absolute error                                                           
print('Mean absolute error: %.2f' % mean_absolute_error(Energies, ytilde))
print(clf.coef_, clf.intercept_)

# The Ridge regression with a hyperparameter lambda = 0.1
_lambda = 0.1
clf_ridge = skl.Ridge(alpha=_lambda).fit(X, Energies)
yridge = clf_ridge.predict(X)
EoS['Eridge']  = yridge
# The mean squared error                               
print("Mean squared error: %.2f" % mean_squared_error(Energies, yridge))
# Explained variance score: 1 is perfect prediction                                 
print('Variance score: %.2f' % r2_score(Energies, yridge))
# Mean absolute error                                                           
print('Mean absolute error: %.2f' % mean_absolute_error(Energies, yridge))
print(clf_ridge.coef_, clf_ridge.intercept_)

fig, ax = plt.subplots()
ax.set_xlabel(r'$\rho[\mathrm{fm}^{-3}]$')
ax.set_ylabel(r'Energy per particle')
ax.plot(EoS['Density'], EoS['Energy'], alpha=0.7, lw=2,
            label='Theoretical data')
ax.plot(EoS['Density'], EoS['Eols'], alpha=0.7, lw=2, c='m',
            label='OLS')
ax.plot(EoS['Density'], EoS['Eridge'], alpha=0.7, lw=2, c='g',
            label='Ridge $\lambda = 0.1$')
ax.legend()
save_fig("EoSfitting")
plt.show()

The above simple polynomial in density $\rho$ gives an excellent fit to the data.

We note also that there is a small deviation between the standard OLS and the Ridge regression at higher densities. We discuss this in more detail below.

Splitting our Data in Training and Test data

It is normal in essentially all Machine Learning studies to split the data in a training set and a test set (sometimes also an additional validation set). Scikit-Learn has an own function for this. There is no explicit recipe for how much data should be included as training data and say test data. An accepted rule of thumb is to use approximately $2/3$ to $4/5$ of the data as training data. We will postpone a discussion of this splitting to the end of these notes and our discussion of the so-called bias-variance tradeoff. Here we limit ourselves to repeat the above equation of state fitting example but now splitting the data into a training set and a test set.

import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

def R2(y_data, y_model):
    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)
def MSE(y_data,y_model):
    n = np.size(y_model)
    return np.sum((y_data-y_model)**2)/n

infile = open(data_path("EoS.csv"),'r')

# Read the EoS data as  csv file and organized into two arrays with density and energies
EoS = pd.read_csv(infile, names=('Density', 'Energy'))
EoS['Energy'] = pd.to_numeric(EoS['Energy'], errors='coerce')
EoS = EoS.dropna()
Energies = EoS['Energy']
Density = EoS['Density']
#  The design matrix now as function of various polytrops
X = np.zeros((len(Density),5))
X[:,0] = 1
X[:,1] = Density**(2.0/3.0)
X[:,2] = Density
X[:,3] = Density**(4.0/3.0)
X[:,4] = Density**(5.0/3.0)
# We split the data in test and training data
X_train, X_test, y_train, y_test = train_test_split(X, Energies, test_size=0.2)
# matrix inversion to find beta
beta = np.linalg.inv(X_train.T.dot(X_train)).dot(X_train.T).dot(y_train)
# and then make the prediction
ytilde = X_train @ beta
print("Training R2")
print(R2(y_train,ytilde))
print("Training MSE")
print(MSE(y_train,ytilde))
ypredict = X_test @ beta
print("Test R2")
print(R2(y_test,ypredict))
print("Test MSE")
print(MSE(y_test,ypredict))

Exercises

Exercise 1: Analytical exercises

In this exercise we derive the expressions for various derivatives of products of vectors and matrices. Such derivatives are central to the optimization of various cost functions. Although we will often use automatic differentiation in actual calculations, to be able to have analytical expressions is extremely helpful in case we have simpler derivatives as well as when we analyze various properties (like second derivatives) of the chosen cost functions. Vectors are always written as boldfaced lower case letters and matrices as upper case boldfaced letters.

Show that

 
$$\frac{\partial (\boldsymbol{b}^T\boldsymbol{a})}{\partial \boldsymbol{a}} = \boldsymbol{b},$$

and

 
$$\frac{\partial (\boldsymbol{a}^T\boldsymbol{A}\boldsymbol{a})}{\partial \boldsymbol{a}} = \boldsymbol{a}^T(\boldsymbol{A}+\boldsymbol{A}^T),$$

and

 
$$\frac{\partial \left(\boldsymbol{x}-\boldsymbol{A}\boldsymbol{s}\right)^T\left(\boldsymbol{x}-\boldsymbol{A}\boldsymbol{s}\right)}{\partial \boldsymbol{s}} = -2\left(\boldsymbol{x}-\boldsymbol{A}\boldsymbol{s}\right)^T\boldsymbol{A},$$

and finally find the second derivative of this function with respect to the vector $\boldsymbol{s}$. If we replace the vector $\boldsymbol{s}$ with the unknown parameters $\boldsymbol{\beta}$ used to define the ordinary least squares method, we end up with the equations that determine these parameters. The matrix $\boldsymbol{A}$ is then the design matrix $\boldsymbol{X}$ and $\boldsymbol{x}$ here has to be replaced with the outputs $\boldsymbol{y}$.

The second derivative of the mean squared error is then proportional to the so-called Hessian matrix $\boldsymbol{H}=\boldsymbol{X}^T\boldsymbol{X}$.

Hint: In these exercises it is always useful to write out with summation indices the various quantities. As an example, consider the function

 
$$f(\boldsymbol{x}) =\boldsymbol{A}\boldsymbol{x},$$

which reads for a specific component $f_i$ (we define the matrix $\boldsymbol{A}$ to have dimension $n\times n$ and the vector $\boldsymbol{x}$ to have length $n$)

 
$$f_i =\sum_{j=0}^{n-1}a_{ij}x_j,$$

which leads to

 
$$\frac{\partial f_i}{\partial x_j}= a_{ij},$$

and written out in terms of the vector $\boldsymbol{x}$ we have

 
$$\frac{\partial f(\boldsymbol{x})}{\partial \boldsymbol{x}}= \boldsymbol{A}.$$

Exercise 2: making your own data and exploring scikit-learn

We will generate our own dataset for a function $y(x)$ where $x \in [0,1]$ and defined by random numbers computed with the uniform distribution. The function $y$ is a quadratic polynomial in $x$ with added stochastic noise according to the normal distribution $\cal {N}(0,1)$. The following simple Python instructions define our $x$ and $y$ values (with 100 data points).

import numpy as np
x = np.random.rand(100,1)
y = 2.0+5*x*x+0.1*np.random.randn(100,1)

1. Write your own code (following the examples under the regression notes) for computing the parametrization of the data set fitting a second-order polynomial.
2. Use thereafter scikit-learn and compare with your own code. Note here that scikit-learn does not include, by default, the intercept. See the discussions on scaling your data in the slides for this week. This type of problems appear in particular if we fit a polynomial with an intercept.
3. Using scikit-learn, compute also the mean squared error, a risk metric corresponding to the expected value of the squared (quadratic) error defined as

 
$$MSE(\boldsymbol{y},\boldsymbol{\tilde{y}}) = \frac{1}{n} \sum_{i=0}^{n-1}(y_i-\tilde{y}_i)^2,$$

and the $R^2$ score function. If $\tilde{\boldsymbol{y}}_i$ is the predicted value of the $i-th$ sample and $y_i$ is the corresponding true value, then the score $R^2$ is defined as

 
$$R^2(\boldsymbol{y}, \tilde{\boldsymbol{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i - \tilde{y}_i)^2}{\sum_{i=0}^{n - 1} (y_i - \bar{y})^2},$$

where we have defined the mean value of $\boldsymbol{y}$ as

 
$$\bar{y} = \frac{1}{n} \sum_{i=0}^{n - 1} y_i.$$

You can use the functionality included in scikit-learn. If you feel for it, you can use your own program and define functions which compute the above two functions. Discuss the meaning of these results. Try also to vary the coefficient in front of the added stochastic noise term and discuss the quality of the fits.

Exercise 3: Split data in test and training data

In this exercise we want you to to compute the MSE for the training data and the test data as function of the complexity of a polynomial, that is the degree of a given polynomial.

The aim is to reproduce Figure 2.11 of Hastie et al. Feel free to read the discussions leading to figure 2.11 of Hastie et al.

Our data is defined by $x\in [-3,3]$ with a total of for example $n=100$ data points. You should try to vary the number of data points $n$ in your analysis.

np.random.seed()
n = 100
# Make data set.
x = np.linspace(-3, 3, n).reshape(-1, 1)
y = np.exp(-x**2) + 1.5 * np.exp(-(x-2)**2)+ np.random.normal(0, 0.1, x.shape)

where $y$ is the function we want to fit with a given polynomial.

a) Write a first code which sets up a design matrix $X$ defined by a fifth-order polynomial and split your data set in training and test data.

b) Write thereafter (using either scikit-learn or your matrix inversion code using for example numpy) and perform an ordinary least squares fitting and compute the mean squared error for the training data and the test data. These calculations should apply to a model given by a fifth-order polynomial. If you compare your own code with _scikit_learn_, not that the latter does not include by default the intercept. See the discussions on scaling your data in the slides for this week.

c) Add now a model which allows you to make polynomials up to degree $15$. Perform a standard OLS fitting of the training data and compute the MSE for the training and test data and plot both test and training data MSE as functions of the polynomial degree. Compare what you see with Figure 2.11 of Hastie et al. Comment your results. For which polynomial degree do you find an optimal MSE (smallest value)?