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hyperparams.py
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#!/usr/bin/python3
MEDIA = "media/"
BASE_PATH = "data/"
SEQ_PATH = BASE_PATH + "sequence/"
STR_PATH = BASE_PATH + "structure/"
CLF_PATH = "clf/"
NPZ_PATH = {
"NPInter" : "npz/NPInter.npz",
"RPI" : {
1807 : "npz/RPI1807.npz",
2241 : "npz/RPI2241.npz",
369 : "npz/RPI369.npz",
488 : "npz/RPI488.npz"
},
"API" : {
"A_train" : "npz/API_A_train.npz",
"B_train" : "npz/API_B_train.npz",
"A_test" : "npz/API_A_test.npz",
"B_test" : "npz/API_B_test.npz"
},
"rand" : {
0 : "npz/random_apt0.npz",
1 : "npz/random_apt1.npz",
2 : "npz/random_apt2.npz",
3 : "npz/random_apt3.npz",
4 : "npz/random_apt4.npz",
5 : "npz/random_apt5.npz",
6 : "npz/random_apt6.npz",
7 : "npz/random_apt7.npz",
8 : "npz/random_apt8.npz",
9 : "npz/random_apt9.npz"
},
"genetic" : {
0 : "npz/genetic_apt0.npz",
1 : "npz/genetic_apt1.npz",
2 : "npz/genetic_apt2.npz",
3 : "npz/genetic_apt3.npz",
4 : "npz/genetic_apt4.npz",
5 : "npz/genetic_apt5.npz",
6 : "npz/genetic_apt6.npz",
7 : "npz/genetic_apt7.npz",
8 : "npz/genetic_apt8.npz",
9 : "npz/genetic_apt9.npz",
10 : "npz/genetic_apt10.npz",
11 : "npz/genetic_apt11.npz",
12 : "npz/genetic_apt12.npz",
13 : "npz/genetic_apt13.npz",
14 : "npz/genetic_apt14.npz",
15 : "npz/genetic_apt15.npz",
16 : "npz/genetic_apt16.npz",
17 : "npz/genetic_apt17.npz",
18 : "npz/genetic_apt18.npz",
19 : "npz/genetic_apt19.npz",
20 : "npz/genetic_apt20.npz",
21 : "npz/genetic_apt21.npz",
22 : "npz/genetic_apt22.npz",
23 : "npz/genetic_apt23.npz",
24 : "npz/genetic_apt24.npz",
25 : "npz/genetic_apt25.npz",
26 : "npz/genetic_apt26.npz",
27 : "npz/genetic_apt27.npz",
28 : "npz/genetic_apt28.npz",
29 : "npz/genetic_apt29.npz"
},
"protein" : "npz/protein.npz",
"mix" : "npz/mix.npz"
}
PAIRS_PATH = {
"RECOMMEND" : MEDIA + BASE_PATH + "RECOMMEND.csv",
"ALL" : MEDIA + BASE_PATH + "ALL.csv",
"result" : BASE_PATH + "RECOMMEND.csv",
"all" : BASE_PATH + "ALL.csv",
"recommend" : {
1 : MEDIA + BASE_PATH + "recommend1.csv",
2 : MEDIA + BASE_PATH + "recommend2.csv",
3 : MEDIA + BASE_PATH + "recommend3.csv",
4 : MEDIA + BASE_PATH + "recommend4.csv",
5 : MEDIA + BASE_PATH + "recommend5.csv",
6 : MEDIA + BASE_PATH + "recommend6.csv",
7 : MEDIA + BASE_PATH + "recommend7.csv",
8 : MEDIA + BASE_PATH + "recommend8.csv",
9 : MEDIA + BASE_PATH + "recommend9.csv",
10 : MEDIA + BASE_PATH + "recommend10.csv",
},
"NPInter" : BASE_PATH + "NPInter_pairs.txt",
"RPI" : {
1807 : BASE_PATH + "RPI1807_pairs.txt",
2241 : BASE_PATH + "RPI2241_pairs.txt",
369 : BASE_PATH + "RPI369_pairs.txt",
488 : BASE_PATH + "RPI488_pairs.txt"
},
"API" : {
"A_train" : BASE_PATH + "benchmark_A_train_sequences.csv",
"B_train" : BASE_PATH + "benchmark_B_train_sequences.csv",
"A_test" : BASE_PATH + "benchmark_A_test_sequences.csv",
"B_test" : BASE_PATH + "benchmark_B_test_sequences.csv"
},
"rand" : {
0 : BASE_PATH + "random_apt0.csv",
1 : BASE_PATH + "random_apt1.csv",
2 : BASE_PATH + "random_apt2.csv",
3 : BASE_PATH + "random_apt3.csv",
4 : BASE_PATH + "random_apt4.csv",
5 : BASE_PATH + "random_apt5.csv",
6 : BASE_PATH + "random_apt6.csv",
7 : BASE_PATH + "random_apt7.csv",
8 : BASE_PATH + "random_apt8.csv",
9 : BASE_PATH + "random_apt9.csv"
},
"genetic" : {
0 : BASE_PATH + "genetic_apt0.csv",
1 : BASE_PATH + "genetic_apt1.csv",
2 : BASE_PATH + "genetic_apt2.csv",
3 : BASE_PATH + "genetic_apt3.csv",
4 : BASE_PATH + "genetic_apt4.csv",
5 : BASE_PATH + "genetic_apt5.csv",
6 : BASE_PATH + "genetic_apt6.csv",
7 : BASE_PATH + "genetic_apt7.csv",
8 : BASE_PATH + "genetic_apt8.csv",
9 : BASE_PATH + "genetic_apt9.csv",
10 : BASE_PATH + "genetic_apt10.csv",
11 : BASE_PATH + "genetic_apt11.csv",
12 : BASE_PATH + "genetic_apt12.csv",
13 : BASE_PATH + "genetic_apt13.csv",
14 : BASE_PATH + "genetic_apt14.csv",
15 : BASE_PATH + "genetic_apt15.csv",
16 : BASE_PATH + "genetic_apt16.csv",
17 : BASE_PATH + "genetic_apt17.csv",
18 : BASE_PATH + "genetic_apt18.csv",
19 : BASE_PATH + "genetic_apt19.csv",
20 : BASE_PATH + "genetic_apt20.csv",
21 : BASE_PATH + "genetic_apt21.csv",
22 : BASE_PATH + "genetic_apt22.csv",
23 : BASE_PATH + "genetic_apt23.csv",
24 : BASE_PATH + "genetic_apt24.csv",
25 : BASE_PATH + "genetic_apt25.csv",
26 : BASE_PATH + "genetic_apt26.csv",
27 : BASE_PATH + "genetic_apt27.csv",
28 : BASE_PATH + "genetic_apt28.csv",
29 : BASE_PATH + "genetic_apt29.csv"
}
}
SEQ_PATH = {
"NPInter" : {
"RNA" : SEQ_PATH + "NPinter_rna_seq.fa",
"Protein" : SEQ_PATH + "NPinter_protein_seq.fa"
},
"RPI" : {
1807 : {
"RNA" : SEQ_PATH + "RPI1807_rna_seq.fa",
"Protein" : SEQ_PATH + "RPI1807_protein_seq.fa"
},
2241 : {
"RNA" : SEQ_PATH + "RPI2241_rna_seq.fa",
"Protein" : SEQ_PATH + "RPI2241_protein_seq.fa"
},
369 : {
"RNA" : SEQ_PATH + "RPI369_rna_seq.fa",
"Protein" : SEQ_PATH + "RPI369_protein_seq.fa"
},
488 : {
"RNA" : SEQ_PATH + "RPI488_rna_seq.fa",
"Protein" : SEQ_PATH + "RPI488_protein_seq.fa"
}
}
}
PIC_PATH = {
"randomForests": {
"A": CLF_PATH + "randomForests_A.pickle",
"B": CLF_PATH + "randomForests_B.pickle"
},
"mix_randomForests": CLF_PATH + "mix_randomForests.pickle"
,
"svm": {
"A": CLF_PATH + "svm_A.pickle",
"B": CLF_PATH + "svm_B.pickle"
},
"NaiveBayesClassifier": {
"A": CLF_PATH + "NaiveBayesClassifier_A.pickle",
"B": CLF_PATH + "NaiveBayesClassifier_B.pickle"
},
"BaggingLinearsvmClassifier": {
"A": CLF_PATH + "BaggingLinearsvmClassifier_A.pickle",
"B": CLF_PATH + "BaggingLinearsvmClassifier_B.pickle"
},
"BaggingKNeighborsClassifier": {
"A": CLF_PATH + "BaggingKNeighborsClassifier_A.pickle",
"B": CLF_PATH + "BaggingKNeighborsClassifier_B.pickle"
},
"GradientBoost": {
"A": CLF_PATH + "GradientBoost_A.pickle",
"B": CLF_PATH + "GradientBoost_B.pickle"
},
"BaggingRandomForestClassifier": {
"A": CLF_PATH + "BaggingRandomForestClassifier_A.pickle",
"B": CLF_PATH + "BaggingRandomForestClassifier_B.pickle"
},
"Voting": {
"A": CLF_PATH + "Voting_A.pickle",
"B": CLF_PATH + "Voting_B.pickle"
}
}