DeepMirTar

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:

pseudo-example:

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

Dependencies:

1), python 2.7, latest version

2), theano, latest version

Further reading:

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