Stacked denoising autoencoder (SdA) code of "Deep learning based functional site-level and UTR-level human miRNA target prediction". The code was rewritten from www.deeplearning.net
The usage of the SdA is similar to sklean:
from SdA_wm import SdA
sda_classifier = SdA()
sda_classifier.pretraining(train_x)
sda_classifier.finetuning(train_x, train_y, valid_x, valid_y) # the valid set is used to optimize the parameters
y_pred = sda_classifier.predict(test_y)
More detaild example, see test_SdA.py
1), python 2.7, latest version
2), theano, latest version
1), A collection of miRNA target gene prediction papers and some miRNA related databases.
https://github.com/Bjoux2/Existing-miRNA-target-gene-prediction-papers
2), Deep-Learning-in-Bioinformatics-Papers-Reading-Roadmap
https://github.com/Bjoux2/Deep-Learning-in-Bioinformatics-Papers-Reading-Roadmap