PROGRAM: BiwalkLDA
AUTHOR: Jialu Hu and Yiqun Gao
EMAIL: jhu@nwpu.edu.cn, yiqun.gao@nwpu-bioinformatics.com
Copyright (MTLAB) <2018>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
########################################################################################### This section introduces functions of different files.
1.Dataset
disease_Name.txt：The name of all the diseases
lncRNA_Name.txt：The name of all the lncRNA-disease
interMatrix.mat：Known lncRNA-disease associations
disSim_Jaccard.mat：Disease similairty calculate by gene ontology annotations information
2.Code
BiWalkLDA.m: BiwalkLDA framework to predict potential lncRNA-disease association
birandom.m: Bi-random walk algorithm
Similarity.m: Calculate Gaussian interaction profile kernel similarity for disease and lncRNA
normFun.m: Laplacian normalization ########################################################################################### This section introduces how to run BiWalkLDA to make prediction
1.Download souce code from https://github.com/screamer/BiwalkLDA
2.Open MATLAB and enter the folder ./Code
3.Run command ‘predict_result = BiWalkLDA(alpha, beta, left, right)’. The higher the value of predict_result(i, j), the higher the possibility of the existence of potential association between lncRNA l(i) and disease d(j).
Notice: the path of the association data can be change in BiWalkLDA.m