From 6591ae8c20e4610094a41616ed29b4cc0fdaede0 Mon Sep 17 00:00:00 2001 From: Apostolos Chalkis Date: Tue, 8 Feb 2022 15:25:40 +0200 Subject: [PATCH] Implement biomass sampling experiments for metabolic networks in C++ (#197) * implement biomass sampling experiments * modify circleci/config.yml * fix bug in log-concave tests * change test function name --- test/CMakeLists.txt | 3 + test/logconcave_sampling_test.cpp | 111 +++++++---- .../e_coli_biomass_function.txt | 1 + test/metabolic_full_dim/polytope_e_coli.ine | 180 ++++++++++++++++++ 4 files changed, 263 insertions(+), 32 deletions(-) create mode 100644 test/metabolic_full_dim/e_coli_biomass_function.txt create mode 100644 test/metabolic_full_dim/polytope_e_coli.ine diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 5679abfb8..2971a46c6 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -172,6 +172,7 @@ else () include_directories (BEFORE ../include/lp_oracles) include_directories (BEFORE ../include/nlp_oracles) include_directories (BEFORE ../include/misc) + include_directories (BEFORE ../test) #for Eigen if (${CMAKE_VERSION} VERSION_LESS "3.12.0") @@ -295,6 +296,8 @@ else () COMMAND logconcave_sampling_test -tc=hmc) add_test(NAME logconcave_sampling_test_uld COMMAND logconcave_sampling_test -tc=uld) + add_test(NAME logconcave_sampling_test_exponential_biomass_sampling + COMMAND logconcave_sampling_test -tc=exponential_biomass_sampling) add_executable (simple_mc_integration simple_mc_integration.cpp $) add_test(NAME simple_mc_integration_over_limits diff --git a/test/logconcave_sampling_test.cpp b/test/logconcave_sampling_test.cpp index abe9380fe..f8f6901cd 100644 --- a/test/logconcave_sampling_test.cpp +++ b/test/logconcave_sampling_test.cpp @@ -703,7 +703,7 @@ void benchmark_polytope_linear_program_optimization( bool rounding=false, bool centered=true, unsigned int max_draws=80000, - unsigned int num_burns=20000) { + unsigned int num_burns=10000) { typedef Cartesian Kernel; typedef std::vector pts; typedef boost::mt19937 RNGType; @@ -756,6 +756,8 @@ void benchmark_polytope_linear_program_optimization( GaussianRDHRWalk::Walk gaussian_walk(P, x0, lp_params.L, rng); int n_warmstart_samples = 100; + std::cout << "Warm start" << std::endl; + for (int i = 0; i < n_warmstart_samples; i++) { gaussian_walk.apply(P, x0, lp_params.L, walk_length, rng); } @@ -788,14 +790,15 @@ void benchmark_polytope_linear_program_optimization( hmc.apply(rng, walk_length); } + hmc.solver->eta = hmc.solver->eta*NT(10); + hmc.disable_adaptive(); + std::cout << std::endl; - std::cout << "Optimizing" << std::endl; - unsigned int num_phases = 0; + std::cout << "Sampling" << std::endl; + unsigned int num_phases = 1; auto start = std::chrono::high_resolution_clock::now(); - for (unsigned int j = 0; j < max_phases; j++) { - num_phases++; - std::cout << "Temperature " << opt_params.T << std::endl; + for (unsigned int j = 0; j < 1; j++) { for (unsigned int i = 0; i < max_actual_draws; i++) { hmc.apply(rng, walk_length); if (f_lp(minimum) >= f_lp(hmc.x)) { @@ -813,12 +816,12 @@ void benchmark_polytope_linear_program_optimization( NT ETA = (NT) std::chrono::duration_cast(stop - start).count(); - std::cerr << "Min LP Value: " << f_lp(minimum) << std::endl; + std::cerr << "Min biomass Value: " << f_lp(minimum) << std::endl; std::cerr << "Argmin: " << minimum.getCoefficients().transpose() << std::endl; - std::cerr << "Average ETA: " << ETA / (NT) num_phases << std::endl; - std::cerr << "Average Time per Independent sample: " << ETA / total_min_ess << std::endl; - std::cerr << "Average Max PSRF: " << total_max_psrf / (NT) num_phases << std::endl; - std::cerr << "Average Min ESS: " << total_min_ess / (NT) num_phases << std::endl; + std::cerr << "ETA: " << ETA / (NT) num_phases << std::endl; + std::cerr << "Time per Independent sample: " << total_min_ess / ETA << std::endl; + std::cerr << "Max PSRF: " << total_max_psrf / (NT) num_phases << std::endl; + std::cerr << "Min ESS: " << total_min_ess / (NT) num_phases << std::endl; std::cerr << "Average number of reflections: " << (1.0 * hmc.solver->num_reflections) / hmc.solver->num_steps << std::endl; std::cerr << "Step size (final): " << hmc.solver->eta << std::endl; @@ -893,10 +896,10 @@ void call_test_benchmark_polytopes_grid_search() { std::make_tuple(generate_cube(100, false), "100_cube", false), std::make_tuple(generate_prod_simplex(50, false), "50_prod_simplex", false), std::make_tuple(generate_birkhoff(10), "10_birkhoff", false), - std::make_tuple(read_polytope("./metabolic_full_dim/polytope_iAB_RBC_283.ine"), "iAB_RBC_283", true), - std::make_tuple(read_polytope("./metabolic_full_dim/polytope_iAT_PLT_636.ine"), "iAT_PLT_636", true), - std::make_tuple(read_polytope("./metabolic_full_dim/polytope_e_coli.ine"), "e_coli", true), - std::make_tuple(read_polytope("./metabolic_full_dim/polytope_recon2.ine"), "recon2", true) + std::make_tuple(read_polytope("metabolic_full_dim/polytope_iAB_RBC_283.ine"), "iAB_RBC_283", true), + std::make_tuple(read_polytope("metabolic_full_dim/polytope_iAT_PLT_636.ine"), "iAT_PLT_636", true), + std::make_tuple(read_polytope("metabolic_full_dim/polytope_e_coli.ine"), "e_coli", true), + std::make_tuple(read_polytope("metabolic_full_dim/polytope_recon2.ine"), "recon2", true) }; Hpolytope P; @@ -998,30 +1001,74 @@ void call_test_benchmark_spectrahedra_grid_search() { } +template +Point load_biomass_function(std::string name) +{ + std::vector v1; + std::string line; + NT element; + + std::ifstream myFile(name); + while(std::getline(myFile, line)) + { + std::istringstream lineStream(line); + + while(lineStream >> element) { + v1.push_back(element); + } + } + Point biomass_function = Point(v1.size(), v1); + NT length = biomass_function.length(); + biomass_function *= (NT(1) / length); + return biomass_function; +} + +inline bool exists_check (const std::string& name) { + std::ifstream f(name.c_str()); + return f.good(); +} + template -void call_test_optimization() { +void call_test_exp_sampling() { typedef Cartesian Kernel; typedef typename Kernel::Point Point; typedef HPolytope Hpolytope; + std::string name; + std::vector> polytopes; + + + if (exists_check("metabolic_full_dim/e_coli_biomass_function.txt") && exists_check("metabolic_full_dim/polytope_e_coli.ine")){ + Point biomass_function_e_coli = load_biomass_function("metabolic_full_dim/e_coli_biomass_function.txt"); + polytopes.push_back(std::make_tuple(read_polytope("metabolic_full_dim/polytope_e_coli.ine"), biomass_function_e_coli, "e_coli", true)); + } - std::vector> polytopes{ - std::make_tuple(generate_cube(100, false), "100_cube", false), - std::make_tuple(read_polytope("./metabolic_full_dim/polytope_e_coli.ine"), "e_coli", true), - }; + if (exists_check("metabolic_full_dim/iAT_PTL_636_biomass_function.txt") && exists_check("metabolic_full_dim/polytope_iAT_PTL_636.ine")){ + Point biomass_function_iAT = load_biomass_function("metabolic_full_dim/iAT_PTL_636_biomass_function.txt"); + polytopes.push_back(std::make_tuple(read_polytope("metabolic_full_dim/polytope_iAT_PTL_636.ine"), biomass_function_iAT, "iAT_PTL_636", true)); + } + + if (exists_check("metabolic_full_dim/recon1_function.txt") && exists_check("metabolic_full_dim/polytope_recon1.ine")){ + Point biomass_function_recon1 = load_biomass_function("metabolic_full_dim/recon1_biomass_function.txt"); + polytopes.push_back(std::make_tuple(read_polytope("metabolic_full_dim/polytope_recon1.ine"), biomass_function_recon1, "recon1", true)); + } Hpolytope P; - std::string name; std::ofstream outfile; + typedef BoostRandomNumberGenerator RNGType; - for (std::tuple polytope_tuple : polytopes) { - P = std::get<0>(polytope_tuple); - name = std::get<1>(polytope_tuple); - std::cerr << name << std::endl; - P.normalize(); - Point coeffs = Point::all_ones(P.dimension()); - for (unsigned int walk_length = 500; walk_length <= P.dimension(); walk_length += P.dimension() / 10) { - benchmark_polytope_linear_program_optimization(coeffs, P, 0, NT(-1), walk_length, false); - } + for (std::tuple polytope_tuple : polytopes) { + P = std::get<0>(polytope_tuple); + name = std::get<2>(polytope_tuple); + + std::cerr << "Model: " + name << std::endl; + std::cout<< "Dimension of " + name + ": " <(polytope_tuple); + for (unsigned int walk_length = P.dimension(); walk_length <= 2*P.dimension(); walk_length += P.dimension()) { + benchmark_polytope_linear_program_optimization(coeffs, P, 0, NT(-1), walk_length, false); + } } } @@ -1145,8 +1192,8 @@ TEST_CASE("uld") { call_test_uld(); } -TEST_CASE("optimization") { - call_test_optimization(); +TEST_CASE("exponential_biomass_sampling") { + call_test_exp_sampling(); } TEST_CASE("benchmark_hmc") { diff --git a/test/metabolic_full_dim/e_coli_biomass_function.txt b/test/metabolic_full_dim/e_coli_biomass_function.txt new file mode 100644 index 000000000..c0c35928b --- /dev/null +++ b/test/metabolic_full_dim/e_coli_biomass_function.txt @@ -0,0 +1 @@ +1.057595362706991726e-01 6.268231060406626726e-04 5.417130007052790575e-01 -4.161378433635810614e-01 -2.634451558388141157e-01 -1.377859647362443540e-01 -1.239169700599200043e-02 -1.771478818636848418e+00 -1.474689492379328559e+00 3.575169148021269949e-01 -1.913772250344042547e+01 1.261758376970891285e-02 -1.425712605922182963e+00 2.234425519598324783e+01 2.942928129761246510e+02 8.469069143284598056e+01 1.059563561026396172e+01 -7.351985582038952316e+01 1.377496801177623098e+01 1.319707473523769181e+02 -3.196840752498849625e+01 -7.523019962729542875e+00 -1.761179600696947745e+01 -6.982659339018495892e+00 \ No newline at end of file diff --git a/test/metabolic_full_dim/polytope_e_coli.ine b/test/metabolic_full_dim/polytope_e_coli.ine new file mode 100644 index 000000000..5d56d8a0c --- /dev/null +++ b/test/metabolic_full_dim/polytope_e_coli.ine @@ -0,0 +1,180 @@ +filename +begin +174 25 real +987.48761136 0.21041897 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