diff --git a/.gitignore b/.gitignore index c795b05..30412e4 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,3 @@ -build \ No newline at end of file +build +demo/test.cpp +debug.log \ No newline at end of file diff --git a/data/siRNA/Huesken.csv b/data/siRNA/Huesken.csv new file mode 100644 index 0000000..769789e --- /dev/null +++ b/data/siRNA/Huesken.csv @@ -0,0 +1,2432 @@ +NASID,GuideStrand,TrainingAll2182,TrainingAll_Human1744,TrainingHumanE2s1229,TrainingRodent438,TrainingRandom1091A,TrainingRandom727A,TrainingRandom545A,TrainingRandom218A,TestingAll249,TestingAll_Human198,TestingHumanE2s139,TestingRodent51,NormalizedInhibitoryActivityb +16802,CUAAUAUGUUAAUUGAUUUat,1,1,0,0,1,0,0,0,0,0,0,0,0.462 +16803,AAUAUGUUAAUUGAUUUAUac,1,1,0,0,0,0,0,0,0,0,0,0,0.384 +16804,GAUUUAUACAAUUCCUUUCaa,0,0,0,0,0,0,0,0,1,1,0,0,0.514 +16805,CAAUUCCUUUCAAUUUUAUct,1,1,0,0,0,0,0,0,0,0,0,0,0.364 +16807,CAGACCAAAAUUAAAUAAGaa,1,1,0,0,0,1,1,0,0,0,0,0,0.522 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+CAUUGUAAGGGUAGCCACUgg +UGUAAGGGUAGCCACUGGGga +GUAAGGGUAGCCACUGGGGaa +GUAGCCACUGGGGAACUCUag +UAGCCACUGGGGAACUCUAgc +GCCACUGGGGAACUCUAGCga +CCACUGGGGAACUCUAGCGag +GAACUCUAGCGAGAGCUUAta +UCUAGCGAGAGCUUAUACCtc +GAGAGCUUAUACCUCAGGUct +GAGCUUAUACCUCAGGUCUtc +AGCUUAUACCUCAGGUCUUca +CCUCAGGUCUUCAUAUACUgt +CUCAGGUCUUCAUAUACUGtt +UCAGGUCUUCAUAUACUGUtc +AGGUCUUCAUAUACUGUUCca +CUUCAUAUACUGUUCCAGCtg +UUCAUAUACUGUUCCAGCUgc +UAUACUGUUCCAGCUGCUCca +ACUGUUCCAGCUGCUCCAUgg +CCAGCUGCUCCAUGGAUGGtc +CAGCUGCUCCAUGGAUGGUcc \ No newline at end of file diff --git a/demo/test.cpp b/demo/test.cpp index ba4ae86..b4389fd 100644 --- a/demo/test.cpp +++ b/demo/test.cpp @@ -25,28 +25,28 @@ int main(int argc, char const *argv[]) int output_size = 4; int input_size = 84; int clausePerOutput = 500; // Only represent the number of clauses that have same polarity. - double dropoutRatio = 0.0; + double dropoutRatio = 0.5; vector> train_seqs(train_data_size, vector(input_size, 0)); vector> train_scores(train_data_size, vector(output_size, 0)); vector> test_seqs(test_data_size, vector(input_size, 0)); vector> test_scores(test_data_size, vector(output_size, 0)); - parse_huesken_seqs("/home/data/siRNA/e2s/e2s_training_seq.csv", train_seqs); - parse_huesken_scores("/home/data/siRNA/e2s/e2s_training_efficiency.csv", train_scores); - parse_huesken_seqs("/home/data/siRNA/e2s/e2s_test_seq.csv", test_seqs); - parse_huesken_scores("/home/data/siRNA/e2s/e2s_test_efficiency.csv", test_scores); + parse_huesken_seqs("../data/siRNA/e2s/e2s_training_seq.csv", train_seqs); + parse_huesken_scores("../data/siRNA/e2s/e2s_training_efficiency.csv", train_scores); + parse_huesken_seqs("../data/siRNA/e2s/e2s_test_seq.csv", test_seqs); + parse_huesken_scores("../data/siRNA/e2s/e2s_test_efficiency.csv", test_scores); TsetlinMachine::MachineArgs mArgs; mArgs.clausePerOutput = clausePerOutput; mArgs.dropoutRatio = dropoutRatio; mArgs.inputSize = input_size; mArgs.outputSize = output_size; - mArgs.sLow = 10.0f; - mArgs.sHigh = 20.0f; - mArgs.T = 400; + mArgs.sLow = 2.0f; + mArgs.sHigh = 100.0f; + mArgs.T = 928; TsetlinMachine tm(mArgs); tm.load(train_seqs,train_scores); - for (int i = 0; i < 100; i++) + for (int i = 0; i < 10; i++) { auto start = std::chrono::high_resolution_clock::now(); tm.train(1); diff --git a/demo/xor.cpp b/demo/xor.cpp index bc7f9a2..1a8d4ec 100644 --- a/demo/xor.cpp +++ b/demo/xor.cpp @@ -34,7 +34,7 @@ int main() { }; TsetlinMachine::MachineArgs mArgs; mArgs.clausePerOutput = 10; - mArgs.dropoutRatio = 0; + mArgs.dropoutRatio = 0.5; mArgs.inputSize = 2; mArgs.outputSize = 2; mArgs.sLow = 4.0f; @@ -42,17 +42,17 @@ int main() { mArgs.T = 4; TsetlinMachine tm(mArgs); - tm.load(inputs, transpose(outputs)); + tm.load(inputs, outputs); vector> prediction; clock_t start = clock(); - for (int i = 0; i < 100000; i++) + for (int i = 0; i < 10000; i++) { tm.train(1); } clock_t duration = clock() - start; std::cout<< duration/(double)CLOCKS_PER_SEC <