/deepMiRGene

DeepMiRGene

Primary LanguagePython

deepMiRGene

Deep Recurrent Neural Network-Based Identification of Precursor microRNAs

Park, Seunghyun, et al. "Deep Recurrent Neural Network-Based Identification of Precursor microRNAs." Advances in Neural Information Processing Systems. 2017.

http://papers.nips.cc/paper/6882-deep-recurrent-neural-network-based-identification-of-precursor-micrornas

//

Usage: python inference/deepMiRGene.py -i <input file> -o <output file>

  • input file: fasta format
  • output file: 0 (true pre-miRNA) or 1 (pseudo pre-miRNA)

Dependencies:

  1. biopython http://biopython.org/wiki/Download

  2. RNAfold (python version) https://www.tbi.univie.ac.at/RNA/#download

  3. sklearn http://scikit-learn.org/stable/install.html

  4. Keras https://keras.io/#installation

  • theono backended

** Reproduce

  1. reproduce/cv.py
  • cross-validation results for the human and cross-species dataset (Table 2)
  1. reproduce/test.py (human and cross-species)
  • test results for the human and cross-species dataset (Table 2)
  1. reproduce/test_new.py (new)
  • test results for the new dataset (Table 3)