Book Image

Large Scale Machine Learning with Python

By : Bastiaan Sjardin, Alberto Boschetti
Book Image

Large Scale Machine Learning with Python

By: Bastiaan Sjardin, Alberto Boschetti

Overview of this book

Large Python machine learning projects involve new problems associated with specialized machine learning architectures and designs that many data scientists have yet to tackle. But finding algorithms and designing and building platforms that deal with large sets of data is a growing need. Data scientists have to manage and maintain increasingly complex data projects, and with the rise of big data comes an increasing demand for computational and algorithmic efficiency. Large Scale Machine Learning with Python uncovers a new wave of machine learning algorithms that meet scalability demands together with a high predictive accuracy. Dive into scalable machine learning and the three forms of scalability. Speed up algorithms that can be used on a desktop computer with tips on parallelization and memory allocation. Get to grips with new algorithms that are specifically designed for large projects and can handle bigger files, and learn about machine learning in big data environments. We will also cover the most effective machine learning techniques on a map reduce framework in Hadoop and Spark in Python.
Table of Contents (17 chapters)
Large Scale Machine Learning with Python
About the Authors
About the Reviewer

Explaining scalability in detail

Even if the hype now is about big data, large datasets existed long before the term itself had been coined. Large collections of texts, DNA sequences, and vast amounts of data from radio telescopes have always represented a challenge for scientists and data analysts. As most machine learning algorithms have a computational complexity of O(n2) or even O(n3), where n is the number of training instances, the challenge from massive datasets has been previously faced by data scientists and analysts by resorting to data algorithms that could be more efficient. A machine learning algorithm is deemed scalable when it can work after an appropriate setup, in case of large datasets. A dataset can be large because of a large number of cases or variables, or because of both, but a scalable algorithm can deal with it in an efficient way as its running time increases almost linearly accordingly to the size of the problem. Therefore, it is just a matter of exchanging 1:1 more time (or more computational power) with more data. Instead, a machine learning algorithm doesn't scale if it's faced with large amounts of data; it simply stops working or operates with a running time that increases in a nonlinear way, for instance, exponentially, thus making learning unfeasible.

The introduction of cheap data storage, a large RAM, and multiprocessor CPU dramatically changed everything, increasing the ability of single laptops to analyze large amounts of data. Another big game changer arrived on the scene in the past years, shifting the attention from single powerful machines to clusters of commodity computers (cheaper, easily available machines). This big change has been the introduction of MapReduce and the open source framework Apache Hadoop with its Hadoop Distributed File System (HDFS) and, in general, of parallel computation on networks of computers.

In order to figure out how both of these changes deeply and positively affected your capabilities of solving your large scale problems, we should first start from what actually prevented you (and still prevents, depending on how massive is your problem) from analyzing large datasets.

No matter what your problem is, you will eventually find out that you cannot analyze your data because of any of these limits:

  • Computing affecting the time taken to execute the analysis

  • I/O affecting how much of your data you can take from storage to memory in a time unit

  • Memory affecting how much large data you can process at a time

Your computer has limitations that will determine if you can learn from your data and how long it will take before you hit a wall. Computing limitations occur in many intensive calculations, I/O problems will bottleneck your prompt access to data, and finally memory limitations can constraint you to take on only a part of your data, thus limiting the kind of matrix computations that you may have access to or the precision or even exactness of your estimations.

Each of these hardware limitations will also affect you differently in severity with regard to the data you are analyzing:

  • Tall data, which is characterized by a large number of cases

  • Wide data, which is characterized by a large number of features

  • Tall and wide data, which has a large number of both cases and features

  • Sparse data, which is characterized by a large number of zero entries or entries that could be transformed into zeros (that is, the data matrix may be tall and/or wide but informative, but not all the matrix entries have informative value)

Finally, it comes down to the algorithm that you are going to use in order to learn from the data. Each algorithm has its own characteristics, being able to map data using a solution differently affected by bias or variance. Therefore, with respect to your problem that, so far, you solved by machine learning, you considered, based on experience or empirical tests, that certain algorithms may work better than others did. With large scale problems, you have to add other and different considerations when deciding on the algorithm:

  • How complex your algorithm is; that is, if the number of rows and columns in your data affects the number of computations in a linear or nonlinear way. Most machine learning solutions are based on algorithms of quadratic or cubic complexity, thus strongly limiting their applicability to big data.

  • How many parameters your model has; here, it's not just a problem of variance of the estimates (overfitting), but of the time it may take to compute them all.

  • If the optimization processes are parallelizable; that is, can you easily split the computations across multiple nodes or CPU cores, or do you have to rely on a single, sequential, optimization process?

  • Should the algorithm learn from all the data at once or can you use single examples or small batches of data instead?

If you cross-evaluate hardware limitations with data characteristics and these kind of algorithms, you'll get a host of possible problematic combinations that can prevent you from getting results from large scale analysis. From a practical point of view, all the problematic combinations can be solved by three approaches:

  • Scaling up, that is, improving performances on a single machine by software or hardware modifications (more memory, faster CPU, faster storage disk, and using GPUs)

  • Scaling out, that is, distributing the computation (and the performances) across multiple machines leveraging outside resources, namely other storage disks and other CPUs (or GPUs)

  • Scaling up and out, that is, taking the best of the scaling up and out solutions together

Making large scale examples

Some motivating examples may make things clearer and more memorable for you. Let's take two simple examples:

  • Being able to predict the click-through rate (CTR) can help you earn quite a lot these days when Internet advertising is so widespread, diffused, and eating large shares of traditional media communication

  • Being able to propose the right information to your customers, when they are searching the products and services offered by your site, could really enhance your chances to sell if you can guess what to put at the top of their results

In both cases, we have quite large datasets as they are produced by users' interactions on the Internet.

Depending on the business that we have in mind (we can imagine some big players here), we are clearly talking of millions of data points per day in both our examples. In the advertising case, data is certainly tall, being a continuous stream of information as the most recent data, more representative of markets and consumers, replaces the older one. In the search engine case, data is wide, being enriched by the feature provided by the results you offered to your customers: for instance, if you are in the travels business, you will have quite a lot of features about hotels, locations, and services offered.

Clearly, scalability is an issue for both these problems:

  • You have to learn from data that is growing every day and you have to learn fast because as you are learning, new data keeps arriving. Yet, you have to deal with data that clearly cannot fit in memory because the matrix is too tall or too large.

  • You frequently need to update your machine learning model in order to accommodate new data. You need an algorithm that can process the information in a timely manner. O(n2) or O(n3) complexities could be impossible for you to handle because of the data quantity; you need some algorithm that can work with lower complexity (such as O(n)) or by dividing the data so that n will be much, much smaller.

  • You have to be able to predict fast because the predictions have to be delivered only to new customers. Again, the complexity of your algorithm does matter.

The scalability problem can be solved in one or multiple ways:

  • Scaling up by reducing the dimensionality of the problem; for instance, in the case of the search engine, by effectively selecting the relevant features to be used

  • Scaling up using the right algorithm; for instance, in the case of advertising data, there are appropriate algorithms to learn effectively from streams

  • Scaling out the learning process by leveraging multiple machines

  • Scaling up the deployment process using multiprocessing and vectorization on a single server effectively

In this book, we will point out for you what kind of practical problems can be solved by each one of the solutions or algorithms proposed. It will become automatic for you to connect a particular constraint in time and execution (CPU, memory, or I/O) to the most suitable solution among the ones that we propose.

Introducing Python

As our treatise will depend on Python—our open source language of choice for this book—we have to stop for a brief moment and present the language before clarifying how Python can easily help you scale up and out with your massive data problem.

Created in 1991 as a general-purpose, interpreted, object-oriented language, Python has slowly and steadily conquered the scientific community and grown into a mature ecosystem of specialized packages for data processing and analysis. It allows you to have uncountable and fast experimentations, easy theory developments, and prompt deployments of scientific applications.

As a machine learning practitioner, you will find using Python interesting for various reasons:

  • It offers a large, mature system of packages for data analysis and machine learning. It guarantees that you will get all that you may need in the course of a data analysis, and sometimes even more.

  • It is very versatile. No matter what your programming background or style is (object-oriented or procedural), you will enjoy programming with Python.

  • If you don't know it yet but you know other languages such as C/C++ or Java well, then it is very simple to learn and use. After you grasp the basics, there's no other better way to learn more than by immediately starting with the coding.

  • It is cross-platform; your solutions will work perfectly and smoothly on Windows, Linux, and macOS systems. You won't have to worry about portability.

  • Although interpreted, it is undoubtedly fast compared to other mainstream data analysis languages such as R and MATLAB (though it is not comparable to C, Java, and the newly emerged Julia language).

  • It can work with in-memory big data because of its minimal memory footprint and excellent memory management. The memory garbage collector will often save the day when you load, transform, dice, slice, save, or discard data using the various iterations and reiterations of data wrangling.


If you are not already an expert (and actually we require some basic knowledge of Python in order to be able to make the most out of this book), you can read everything about the language and find the basic installations files directly from the Python foundations at

Scale up with Python

Python is an interpreted language; it runs the reading of your script from memory and executes it during runtime, thus accessing the necessary resources (files, objects in memory, and so on). Apart from being interpreted, another important aspect to take into consideration when using Python for data analysis and machine learning is that Python is single-threaded. Being single-threaded means that any Python program is executed sequentially from the start to the end of the script and that Python cannot take advantage of the extra processing power offered by the multiple threads and processors likely present in your computer (most computers nowadays are multicore).

Given such a situation, scaling up using Python can be achieved by different strategies:

  • Compiling Python scripts in order to achieve more speed of execution. Though easily possible using, for instance, PyPy—a Just-in-Time (JIT) compiler that can be found at, we actually didn't resort to such a solution in our book because it requires writing algorithms in Python from scratch.

  • Using Python as a wrapping language; thus putting together the operations executed by Python with the execution of external libraries and programs, some capable of multicore processing. In our book, you will find many examples of this when we call specialized libraries such as the Library for Support Vector Machines (LIBSVM) or programs such as Vowpal Wabbit (VW), XGBoost, or H2O in order to execute machine learning activities.

  • Effectively using vectorization techniques, that is, special libraries for matrix computations. This can be achieved using NumPy or pandas, both using computations from GPUs. GPUs are just like multicore CPUs, each one with their own memory and ability to process calculations in parallel (you can figure out that they have multiple tiny cores). Especially when working with neural networks, vectorization techniques based on GPUs can speed up computations incredibly. However, GPUs have their own limitations; first of all, their available memory has a certain I/O in passing your data to their memory and getting the results back to your CPU, and they require parallel programming via a special API, such as CUDA for NVIDIA-manufactured GPUs (so you have to install the appropriate drivers and programs).

  • Reducing a large problem into chunks and solving each chunk one at a time in-memory (divide and conquer algorithms). This leads to the partitioning or subsampling of data from memory or disk and managing approximate solutions of your machine learning problem, which is quite effective. It is important to notice that both partitioning and subsampling can operate for cases and features (and both). If the original data is kept on a disk storage, I/O constraints will become quite determinant of the resulting performances.

  • Effectively leveraging both multiprocessing and multithreading, depending on the learning algorithm that you will be using. Some algorithms will naturally be able to split their operations into parallel ones. In such cases, the only constraint will be your CPU's and your memory (as your data will have to be replicated for every parallel worker that you will be using). Some other algorithms will instead take advantage of multithreading, thus managing more operations at the same time on the same memory blocks.

Scale out with Python

Scaling out solutions simply involve connecting together multiple machines into a cluster. As you connect the machines (scaling out), you can also scale up each one of them using configurations that are more powerful (thus augmenting CPU, memory, and I/O), applying the techniques we mentioned in the previous paragraph and enhancing their performances.

By connecting multiple machines, you can leverage their computational power in a parallel fashion. Your data will be distributed across multiple storage disks/memory, limiting I/O transfers by having each machine work only on its available data (that is, its own storage disk or RAM memory).

In our book, this translates into using outside resources effectively by means of the following:

  • The H2O framework

  • The Hadoop framework and its components, such as HDFS, MapReduce, and Yet Another Resource Negotiator (YARN)

  • The Spark framework on top of Hadoop

Each of these frameworks will be controlled by Python (for instance, Spark by its Python interface named pySpark).