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Deep Learning for Genomics

You're reading from   Deep Learning for Genomics Data-driven approaches for genomics applications in life sciences and biotechnology

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Product type Paperback
Published in Nov 2022
Publisher Packt
ISBN-13 9781804615447
Length 270 pages
Edition 1st Edition
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Author (1):
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Upendra Kumar Devisetty Upendra Kumar Devisetty
Author Profile Icon Upendra Kumar Devisetty
Upendra Kumar Devisetty
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Table of Contents (18) Chapters Close

Preface 1. Part 1 – Machine Learning in Genomics
2. Chapter 1: Introducing Machine Learning for Genomics FREE CHAPTER 3. Chapter 2: Genomics Data Analysis 4. Chapter 3: Machine Learning Methods for Genomic Applications 5. Part 2 – Deep Learning for Genomic Applications
6. Chapter 4: Deep Learning for Genomics 7. Chapter 5: Introducing Convolutional Neural Networks for Genomics 8. Chapter 6: Recurrent Neural Networks in Genomics 9. Chapter 7: Unsupervised Deep Learning with Autoencoders 10. Chapter 8: GANs for Improving Models in Genomics 11. Part 3 – Operationalizing models
12. Chapter 9: Building and Tuning Deep Learning Models 13. Chapter 10: Model Interpretability in Genomics 14. Chapter 11: Model Deployment and Monitoring 15. Chapter 12: Challenges, Pitfalls, and Best Practices for Deep Learning in Genomics 16. Index 17. Other Books You May Enjoy

Introducing RNNs

To address the limitations of FNNs and CNNs regarding sequential data, we need a network that can meet 2 requirements.

  1. It can takes sequences of non-fixed lengths, one element of the sequence at a time.
  2. It must not only identify the nonlocal relationships in the sequence but also remember the most important events that happened before.

This idea led to the development of RNNs, which are a variant of DNN with a feedback loop (hidden state) that can feed the results back into the network and make them part of the final output (Figure 6.3):

Figure 6.3 – Recurrent neural network

RNNs capture previous observations or historical events up to the current timestamp and because the hidden state of the current stamp is the same as the previous timestamp, the computation is recurrent (hence why they are referred to as RNNs):

Figure 6.4 – Difference between a standard neural network (a) and a recurrent...

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