Book Image

Applied Machine Learning and High-Performance Computing on AWS

By : Mani Khanuja, Farooq Sabir, Shreyas Subramanian, Trenton Potgieter
Book Image

Applied Machine Learning and High-Performance Computing on AWS

By: Mani Khanuja, Farooq Sabir, Shreyas Subramanian, Trenton Potgieter

Overview of this book

Machine learning (ML) and high-performance computing (HPC) on AWS run compute-intensive workloads across industries and emerging applications. Its use cases can be linked to various verticals, such as computational fluid dynamics (CFD), genomics, and autonomous vehicles. This book provides end-to-end guidance, starting with HPC concepts for storage and networking. It then progresses to working examples on how to process large datasets using SageMaker Studio and EMR. Next, you’ll learn how to build, train, and deploy large models using distributed training. Later chapters also guide you through deploying models to edge devices using SageMaker and IoT Greengrass, and performance optimization of ML models, for low latency use cases. By the end of this book, you’ll be able to build, train, and deploy your own large-scale ML application, using HPC on AWS, following industry best practices and addressing the key pain points encountered in the application life cycle.
Table of Contents (20 chapters)
1
Part 1: Introducing High-Performance Computing
6
Part 2: Applied Modeling
13
Part 3: Driving Innovation Across Industries

Applying ML to genomics

Before we dive into ML model details, let’s first understand the genomic data, which is stored as DNA in every organism. There are four chemical bases present in DNA, namely Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). They always bond in particular manner for example, Adenine will always bond with Thymine, and Cytosine with Guanine. The combination of these chemical bases is what makes up a DNA sequence, represented by the letters A, T, C, and G. A 20-length example of a DNA sequence is ACTCCACAGTACCTCCGAGA. A single complete sequence of the human genome is around 3 billion base pairs (bp) long and takes about 200 GB of data storage (https://www.science.org/doi/10.1126/science.abj6987).

However, for analyzing the DNA sequence, we don’t need the complete human genome sequence. Usually, we analyze a part of the human DNA; for example, to determine hair growth or skin growth, a lab technician will take a small section of human skin...