Book Image

Deep Learning for Genomics

By : Upendra Kumar Devisetty
Book Image

Deep Learning for Genomics

By: Upendra Kumar Devisetty

Overview of this book

Deep learning has shown remarkable promise in the field of genomics; however, there is a lack of a skilled deep learning workforce in this discipline. This book will help researchers and data scientists to stand out from the rest of the crowd and solve real-world problems in genomics by developing the necessary skill set. Starting with an introduction to the essential concepts, this book highlights the power of deep learning in handling big data in genomics. First, you’ll learn about conventional genomics analysis, then transition to state-of-the-art machine learning-based genomics applications, and finally dive into deep learning approaches for genomics. The book covers all of the important deep learning algorithms commonly used by the research community and goes into the details of what they are, how they work, and their practical applications in genomics. The book dedicates an entire section to operationalizing deep learning models, which will provide the necessary hands-on tutorials for researchers and any deep learning practitioners to build, tune, interpret, deploy, evaluate, and monitor deep learning models from genomics big data sets. By the end of this book, you’ll have learned about the challenges, best practices, and pitfalls of deep learning for genomics.
Table of Contents (18 chapters)
Part 1 – Machine Learning in Genomics
Part 2 – Deep Learning for Genomic Applications
Part 3 – Operationalizing models

What is a genome?

Before we discuss genomes, let’s do a quick Genetics 101. A cell represents the fundamental structural and functional unit of life. DNA contains the instructions that are needed to perform different activities of the cell. DNA is the basis of genetic studies and consists of four building blocks called nucleotides – adenine (A), guanine (G), cytosine (C), and thymine (T), which store information about life. The sequence of DNA is a string of these building blocks, also referred to as bases. DNA has a double-helix structure with two complementary polymers interlaced with each other. In the complementary strand of DNA, A matches with T, and G matches with C, to form base pairs.

A genome represents the full DNA sequence of a cell that contains all the hereditary information. The genome consists of information that is needed to build and maintain the whole living organism. The size of genomes is different from species to species. For example, the human...