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DeepMiRGene
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README.md Update README.md Jun 23, 2018

README.md

deepMiRGene

Deep Recurrent Neural Network-Based Identification of Precursor microRNAs

Seunghyun Park, Seonwoo Min, Hyun-Soo Choi, and Sungroh Yoon, in Proceedings of the Annual Conference on Neural Information Processing Systems (NIPS), Long Beach, USA, December 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

  2. RNAfold (python version)

  3. sklearn

  4. Keras

  • theano 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)
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