bwang-ecnu/deepfe-ppi

DeepFE-PPI

DeepFE-PPI: An integration of deep learning with feature embedding for protein-protein interaction prediction we have reported a novel predictor DeepFE-PPI，a protein-protein interaction prediction method that integrates deep learning and feature embedding.For a given protein-protein pair, we first use Res2Vec to repressnt all residues, and then we regard the feature vector as the input of the network and apply a branch of dense layers to automatically learn diverse hierarchical features. Finally, we use a neural network with four hidden layers to connect their outputs for PPIs prediction.

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DeepFE-PPI uses the following dependencies:

• Python 3.5.2
• Numpy 1.14.1
• Gensim 3.4.0
• HDF5 and h5py
• Pickle
• Scikit-learn 0.19
• Tensorflow 1.2.0
• keras 1.2.0

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Datasets

The main directory contains the directories of S.cerevisiae, Human and five species-specific protein-protein interaction datasets. In each directory, there are:

• The S.cerevisiae core dataset: 5594 positive protein pairs and 5594 negative protein pairs.
• The human dataset: 3899 positive protein pairs and 4262 negative protein pairs.
• Each of five species-specific protein interaction datasets (C. elegans, E. coli, H. sapiens, M. musculus, and H. pylori) contains 4013, 6954, 1412, 313 and 1420 positive protein pairs.

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model

The model directory contains 5 subfolders, with a folder for word2vec models and four folders for deep learning models, and structured as follows:

• c1c2c3: This folder contains a model corresponds to Section " Park and Marcotte’s evaluation scheme".
• dl: This folder have two subfolders:
  • 11188 folder contains the model that the 5-flod cross validation methods executed on the S.cerevisiae core dataset.
  • human folder contains the model that the 5-flod cross validation methods executed on the human dataset.
• rewrite: This folder contains a model corresponds to 'redo_cv_code.py'.
• train_11188_test_5_special: This folder contains a model corresponds to 'train_11188_test_5_special.py'.
• word2vec: This folder contains all word2vec models when Parameter Selection.

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*.py

• 5cv_11188.py: 5-flod cross validation methods on the S.cerevisiae core dataset.
• 5cv_human.py: 5-flod cross validation methods on the human dataset.
• c1c2c3_11188.py: The code corresponds to Section " Park and Marcotte’s evaluation scheme". We redo the special multiple cross-validation method proposed by Park & Marcotte [Park Y, Marcotte EM. Nat Methods. 2012; 9 (12)]
• redo_cv_code.py: We rewrite the cross validation method without any libraries.
• swiss_Res2vec_val_11188.py: Parameter Selection for residue reprsetation and deep learning.
• train_11188_test_5_special.py: Codes that trains on the S.cerevisiae core dataset and tests on five species-specific protein interaction datasets.

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Usage: Run these file from command line.

For example:

python train_11188_test_5_special.py output:

• accuracy_test_Celeg = 100,
• accuracy_test_Ecoli = 100,
• accuracy_test_Hpylo = 100,
• accuracy_test_Hsapi = 100,
• accuracy_test_Mmusc = 100

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Contact us: Any questions about DeepFE-PPI, please email to [email protected].

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This dataset was used in the paper 'DeepFE-PPI: An integration of deep learning with feature embedding for protein-protein interaction prediction' for PPI prediction. For more details, please refer to the paper.