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test.cpp
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test.cpp
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#include <iostream>
#include <cmath>
#include "hmm.h"
#include "data_loading.h"
class Test {
public:
static void test_forward() {
std::cout << ">>> Test forward start. <<<" << std::endl;
const std::string states = "FBBFFBBFBFFBFFB";
const std::string emissions = "562364166532654";
const int N = 2;
const int M = 6;
hidden_markov_chain<N, M> hmm({'F', 'B'}, {'1', '2', '3', '4', '5', '6'});
hmm.estimate_initial_probabilities(states, emissions);
double** alpha = hmm.forward(emissions);
std::cout << "alpha" << std::endl;
for(int i = 0; i < emissions.length(); i++) {
for(int j = 0; j < N; j++) {
std::cout << alpha[i][j] << " ";
}
std::cout << std::endl;
}
delete[] alpha;
std::cout << ">>> Test forward done. <<<" << std::endl;
}
static void test_backward() {
std::cout << ">>> Test backward start. <<<" << std::endl;
const std::string states = "FBBFFBBFBFFBFFB";
const std::string emissions = "562364166532654";
const int N = 2;
const int M = 6;
hidden_markov_chain<N, M> hmm({'F', 'B'}, {'1', '2', '3', '4', '5', '6'});
hmm.estimate_initial_probabilities(states, emissions);
double** beta = hmm.backward(emissions);
std::cout << "beta" << std::endl;
for(int i = 0; i < emissions.length(); i++) {
for(int j = 0; j < N; j++) {
std::cout << beta[i][j] << " ";
}
std::cout << std::endl;
}
delete[] beta;
std::cout << ">>> Test backward done. <<<" << std::endl;
}
static void test_baum_welch_algorithm() {
std::cout << ">>> Test baum_welch_algorithm start. <<<" << std::endl;
const std::string states = "FBBFFBBFBFFBFFB";
const std::string emissions = "562364166532654";
const int N = 2;
const int M = 6;
hidden_markov_chain<N, M> hmm({'F', 'B'}, {'1', '2', '3', '4', '5', '6'});
hmm.estimate_initial_probabilities(states, emissions);
hmm.baum_welch_algorithm(emissions, 1000);
std::cout << ">>> Test baum_welch_algorithm done. <<<" << std::endl;
}
static void test_estimate_initial_probabilities() {
const std::string states = "FBBFFBBFBFFBFFB";
const std::string emissions = "562364166532654";
const int N = 2;
const int M = 6;
hidden_markov_chain<N, M> hmm({'F', 'B'}, {'1', '2', '3', '4', '5', '6'});
hmm.estimate_initial_probabilities(states, emissions);
double states_initial_probs[] = {8/15., 7/15.};
double transition_initial_probs[N][N] = {
{3/7., 5/7.}, //F->F, F->B
{4/7., 2/7.} //B->F, B->B
};
double emission_initial_probs[N][M] = {
{0/8., 0/8., 2/8., 0/8., 3/8., 3/8.},
{1/7., 2/7., 0/7., 2/7., 0/7., 2/7.}
};
if (!is_equal_arrays<N>(states_initial_probs, hmm._states_probabilities))
std::cerr << "Initial states probabilities are not equal!" << std::endl;
if (!is_equal_matrices<N, N>(transition_initial_probs, hmm._transition_probabilities))
std::cerr << "Transition probabilities are not equal!" << std::endl;
if (!is_equal_matrices<N, M>(emission_initial_probs, hmm._emission_probabilities))
std::cerr << "Emission probabilities are not equal!" << std::endl;
std::cout << ">>> Test estimate initial probabilities done. <<<" << std::endl;
}
static void test_convert_islands_to_string() {
const auto emissions = "ACTGCGCGCATTTGCGCTGCA";
std::vector<std::pair<int, int>> islands;
islands.emplace_back(3, 8); // inclusive borders
islands.emplace_back(13, 20);
const auto states_simple = "---++++++----++++++++";
auto states_simple_ = from_islands_to_str(islands, emissions);
if (states_simple != states_simple_)
std::cerr << "Conversion from islands to string (simple) failed! Strings do not match." << std::endl;
const auto states = "actGCGCGCatttGCGCTGCA";
auto states_ = from_islands_to_str(islands, emissions, false);
if (states != states_)
std::cerr << "Conversion from islands to string failed! Strings do not match." << std::endl;
std::cout << ">>> Test convert islands to string done. <<<" << std::endl;
}
static void test_viterbi(){
std::cout << ">>> Test viterbi start. <<<" << std::endl;
const std::string states = "FBBFFBBFBFFBFFB";
const std::string emissions = "562364166532654";
const int N = 2;
const int M = 6;
hidden_markov_chain<N, M> hmm({'F', 'B'}, {'1', '2', '3', '4', '5', '6'});
hmm.estimate_initial_probabilities(states, emissions);
std::string result = hmm.viterbi_algorithm(states);
std::cout << result << std::endl;
std::cout << ">>> Test viterbi done. <<<" << std::endl;
}
static double test_simple(const std::string& train_seq_path,const std::string& train_path,
const std::string& test_seq_path, const std::string& test_path) {
std::cout << ">>> Test simple start. <<<" << std::endl;
std::string train_sequence, train_emissions, test_sequence, test_emissions;
std::tie(train_sequence, train_emissions) = parse_data(train_path, train_seq_path, true);
std::tie(test_sequence, test_emissions) = parse_data(test_path, test_seq_path, true);
hidden_markov_chain<2, 4> hmm({'+', '-'}, {'A', 'C', 'G', 'T'});
hmm.fit(train_sequence, train_emissions, 1);
hmm.print_transition_probabilities_and_emission_probabilities();
auto predicted_emissions = hmm.predict(test_emissions);
std::string hit_or_miss;
double accuracy;
std::tie(accuracy, hit_or_miss) = evaluate(test_sequence, predicted_emissions);
std::cout << "Accuracy: " << accuracy << std::endl;
std::cout << predicted_emissions << std::endl;
std::cout << from_str_to_islands(predicted_emissions) << std::endl;
std::cout << ">>> Test simple done. <<<" << std::endl;
return accuracy;
}
static void test_complex(const std::string& train_seq_path,const std::string& train_path,
const std::string& test_seq_path, const std::string& test_path) {
std::cout << ">>> Test complex start. <<<" << std::endl;
std::string train_sequence, train_emissions, test_sequence, test_emissions;
std::tie(train_sequence, train_emissions) = parse_data(train_path, train_seq_path, false);
std::tie(test_sequence, test_emissions) = parse_data(test_path, test_seq_path, false);
hidden_markov_chain<8, 4> hmm({'a', 'c', 'g', 't', 'A', 'C', 'G', 'T'}, {'A', 'C', 'G', 'T'});
hmm.fit(train_sequence, train_emissions, 1);
hmm.print_transition_probabilities_and_emission_probabilities();
auto predicted_emissions = hmm.predict(test_emissions);
std::string hit_or_miss;
double accuracy;
std::tie(accuracy, hit_or_miss) = evaluate(test_sequence, predicted_emissions);
std::cout << "Accuracy: " << accuracy << std::endl;
std::cout << predicted_emissions << std::endl;
std::cout << from_str_to_islands(predicted_emissions, false) << std::endl;
std::cout << ">>> Test complex done. <<<" << std::endl;
}
static void convert_from_str_to_islands(const std::string& island_path, bool simple=true) {
auto sequence = load_raw(island_path);
auto islands = from_str_to_islands(sequence, simple);
std::cout << islands << std::endl;
}
static void evaluate_islands(const std::string& seq_path, const std::string& true_path,
const std::string& predict_path, bool simple=true) {
// true observations are always saved as indexes, don't tell me twice it's a bad design
std::string sequence, true_obs;
std::tie(true_obs, sequence) = parse_data(true_path, seq_path);
std::string predicted_obs = load_raw(predict_path);
std::string hit_or_miss;
double accuracy;
std::tie(accuracy, hit_or_miss) = evaluate(true_obs, predicted_obs, simple);
std::cout << "Accuracy: " << accuracy << std::endl;
}
private:
template<int N>
static bool is_equal_arrays(double a[N], double b[N]) {
for (auto i = 0; i < N; ++i) {
if (std::abs(a[i] - b[i]) > std::numeric_limits<double>::epsilon()) return false;
}
return true;
}
template<int N, int M>
static bool is_equal_matrices(double a[N][M], double b[N][M]) {
for (auto i = 0; i < N; ++i) {
if (!is_equal_arrays<M>(a[i], b[i])) return false;
}
return true;
}
};
int main() {
// Test::test_estimate_initial_probabilities();
// Test::test_convert_islands_to_string();
// Test::test_create_emission_to_idx_map();
// Test::test_forward();
// Test::test_backward();
// Test::test_baum_welch_algorithm();
// Test::test_viterbi();
// Test::test_mm39_relaxed_simple();
// Test::evaluate_islands(R"(..\data\seven-thrice-nonislands\sequences\chr19_14.txt)", R"(..\data\seven-thrice-nonislands\islands\chr19_14.txt)",
// R"(..\data\seven-thrice-nonislands\predicted\chr19_14_viterbi.txt)", true);
// Test::convert_from_str_to_islands(R"(..\data\seven-thrice-nonislands\predicted\chr19_14_viterbi.txt)", true);
Test::test_simple(R"(..\data\seven-even-islands\sequences\chr19_0.txt)", R"(..\data\seven-even-islands\islands\chr19_0.txt)",
R"(..\data\seven-thrice-nonislands\sequences\chr19_14.txt)", R"(..\data\seven-thrice-nonislands\islands\chr19_14.txt)");
// Test::test_complex(R"(..\data\even\sequences\chr19_0.txt)", R"(..\data\even\islands\chr19_0.txt)",
// R"(..\data\even\sequences\chr19_3.txt)", R"(..\data\even\islands\chr19_3.txt)");
return 0;
}