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Deep learning for genomics - a set of Jupyter notebooks.
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Readme.md
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data_exploration_dna_transcription.ipynb
example_hyperas.ipynb
hyperparameter_cnn1d_dna_transcription.ipynb
keras_cnn1d_dna_transcription.ipynb
keras_sklearn_cnn1d_crp_transcription.ipynb
keras_sklearn_cnn1d_dna_transcription.ipynb
keras_sklearn_cnn1d_dna_transcription_logx.ipynb
keras_sklearn_cnn1d_dna_transcription_powerx.ipynb
keras_sklearn_cnn1d_dna_transcription_quantx.ipynb Created using Colaboratory May 19, 2019
ray_tune_cnn1d_dna_transcription.ipynb

Readme.md

Deep Learning for Genomics

This repository contains Jupyter notebooks and notes for deep learning for genomics. We principally use keras and scikit-learn for deep learning, but other libraries (joblib, ray, tune, hyperas, hyperopt) are used along the way as well.

Predicting DNA Transcription Factor Binding Sites

Exploring the Data

Keras 1D Convolutional Neural Network

Creating the Network

Data Transformations

Hyperparameter Optimization

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