Python 3.7x (may work with earlier versions, not tested)
Sklearn 0.0
Numpy 1.17.0
Pandas 1.2.3
Java environment
1.RankLib-2.16.jar(download)
train:
java -jar RankLib-2.16.jar -train train.txt -ranker 0 -metric2t NDCG@50 -tree 500 -leaf 300 -shrinkage 0.03
-mls 5 -tc 256 -save t_model.txt -out t_out.txt
test:
java -jar RankLib-2.16.jar -load t_model.txt -rank test.txt -indri test_rank.txt
2.index_available.py -- Get the index of the data that satisfies the constraint
3.AAF.py/SAF.py -- Extract features
MSE
CI
Rm2
The characteristics of drugs and proteins are obtained in the same way, and the code only lists one
Some data processing is done with linux commands,the code is simple, therefore the specific code is not listed.
sharing-sharing matrix --data processing.py
rm2 refers to the code in DeepDTA(Öztürk H, Özgür A, Ozkirimli E. DeepDTA: deep drug–target binding affinity prediction[J]. Bioinformatics, 2018, 34(17): i821-i829.)