├── .gitignore ├── LICENSE ├── README.md ├── additive_demo.m ├── data ├── classification │ ├── bach_synth │ │ └── make_synth_classification.m │ ├── bach_synth_c_100.mat │ ├── bach_synth_c_200.mat │ ├── breast.mat │ ├── breast │ │ ├── breast-cancer_scale.mat │ │ ├── breast-cancer_scale.txt │ │ ├── breast.data │ │ ├── breast.names │ │ ├── breast_load.m │ │ └── breast_load2.m │ ├── crabs.mat │ ├── crabs │ │ ├── crabs.dat │ │ ├── crabs_numeric.txt │ │ └── make_crabs.m │ ├── fisherIrisData │ │ └── fisherIrisData.mat │ ├── heart │ │ ├── cleve.mod.txt │ │ ├── heart_raw.mat │ │ ├── process_heart_data.m │ │ ├── processed.cleveland.data │ │ └── processed.cleveland_missing_removed.data │ ├── ionosphere.mat │ ├── ionosphere │ │ ├── clean_ionosphere.m │ │ ├── ionosphere.mat │ │ ├── ionosphere.zip │ │ ├── ionosphere │ │ │ ├── ionosphere-meta.txt │ │ │ ├── ionosphere.mat │ │ │ ├── ionosphere.zip │ │ │ └── uci.ionosphere.data │ │ └── uci.ionosphere.data │ ├── liver │ │ ├── bupa.data │ │ ├── bupa.names.txt │ │ ├── liver_raw.mat │ │ ├── process_heart_data.m │ │ └── process_liver_data.m │ ├── pima.mat │ ├── preprocess │ │ ├── make_pima.m │ │ └── sonar_all.data │ ├── r_breast.mat │ ├── r_heart.mat │ ├── r_ionosphere.mat │ ├── r_liver.mat │ ├── r_pima.mat │ ├── r_sanity_easy.mat │ ├── r_sanity_hard.mat │ ├── r_sonar.mat │ ├── sanity_easy.mat │ ├── sanity_hard.mat │ ├── sonar.mat │ └── soy │ │ ├── soy.mat │ │ └── soy.zip ├── randomize_dataset_orders.m └── regression │ ├── abalone │ ├── abalone_raw.data │ ├── description.txt │ └── parse_abalone.m │ ├── abalone_500.mat │ ├── abalone_all.mat │ ├── add10 │ ├── add10_raw.txt │ │ └── Dataset.data │ ├── description.txt │ └── make_smaller.m │ ├── add_1024.mat │ ├── add_256.mat │ ├── add_512.mat │ ├── autompg │ ├── autompg.mat │ ├── autompg.txt │ ├── autompg.zip │ └── autompgMakeData.m │ ├── bach_synth │ └── make_bach_synth.m │ ├── bach_synth_r_100.mat │ ├── bach_synth_r_200.mat │ ├── concrete │ ├── .~lock.Concrete_Data.csv# │ ├── Concrete_Data.csv │ ├── Concrete_Data.xls │ ├── concrete_raw.mat │ ├── feature_names.m │ └── process_concrete_data.m │ ├── housing.mat │ ├── prostate.mat │ ├── prostate │ ├── prostate.data │ ├── prostate.mat │ ├── prostate.readme.txt │ ├── prostate.txt │ ├── prostate.zip │ ├── prostateDataMake.m │ └── prostateStnd.mat │ ├── pumadyn-8nh │ ├── Dataset.data │ ├── Dataset.data.gz │ ├── Dataset.spec │ ├── accel │ │ ├── Prototask.data │ │ ├── Prototask.data.gz │ │ ├── Prototask.spec │ │ └── std.prior │ └── make_smaller.m │ ├── pumadyn1024.mat │ ├── pumadyn256.mat │ ├── pumadyn512.mat │ ├── pumadyn8nh.mat │ ├── r_concrete_100.mat │ ├── r_concrete_1030.mat │ ├── r_concrete_500.mat │ ├── r_housing.mat │ ├── r_pumadyn512.mat │ ├── r_servo.mat │ ├── r_solar_500.mat │ ├── r_solar_all.mat │ ├── servo.mat │ ├── servo │ ├── servo.mat │ └── servo.zip │ └── solar │ ├── flare.data2 │ ├── flare.names │ ├── multinomial_to_1_of_k.m │ └── process_solar_data.m ├── experiments ├── compile_all_results.m ├── compile_results.m ├── define_datasets_and_methods.m ├── run_all_experiments.m ├── run_experiment_set.m ├── run_one_experiment.m └── run_one_fold.m ├── figures ├── draw_2d_kernels.m ├── draw_3d_kernels.m ├── draw_cement_interaction_plots.m ├── draw_interaction_plots2.m ├── plot_1st_order_interactions.m ├── plot_1st_order_interactions_c.m ├── plot_2nd_order_interactions.m ├── plot_3d_density.m ├── plot_3rd_order_interactions.m ├── poster_synthetic_1st_order_censored.m ├── synthetic_1st_order_censored.m ├── synthetic_bach_plots.m ├── test_3d_density.m ├── test_3d_density2.m └── voxel.m ├── gpml ├── .octaverc ├── Copyright ├── README ├── barrier_fct.m ├── cov │ ├── covADD.m │ ├── covConst.m │ ├── covFITC.m │ ├── covLIN.m │ ├── covLINard.m │ ├── covLINone.m │ ├── covMask.m │ ├── covMaterniso.m │ ├── covNNone.m │ ├── covNoise.m │ ├── covPPiso.m │ ├── covPeriodic.m │ ├── covPoly.m │ ├── covProd.m │ ├── covRQard.m │ ├── covRQiso.m │ ├── covSEard.m │ ├── covSEiso.m │ ├── covSEisoU.m │ ├── covSEiso_length.m │ ├── covSEiso_var.m │ ├── covScale.m │ └── covSum.m ├── covFunctions.m ├── doc │ ├── README │ ├── changelog │ ├── checkmark.png │ ├── demoClassification.m │ ├── demoRegression.m │ ├── f0.gif │ ├── f1.gif │ ├── f2.gif │ ├── f3.gif │ ├── f4.gif │ ├── f5.gif │ ├── f6.gif │ ├── gpml_randn.m │ ├── index.html │ ├── manual.pdf │ ├── style.css │ ├── usageClassification.m │ ├── usageCov.m │ ├── usageMean.m │ └── usageRegression.m ├── gp.m ├── inf │ ├── infEP.m │ ├── infExact.m │ ├── infFITC.m │ ├── infLOO.m │ ├── infLaplace.m │ └── infVB.m ├── infMethods.m ├── lik │ ├── likErf.m │ ├── likGauss.m │ ├── likLaplace.m │ ├── likLogistic.m │ ├── likSech2.m │ └── likT.m ├── likFunctions.m ├── mean │ ├── meanConst.m │ ├── meanLinear.m │ ├── meanMask.m │ ├── meanOne.m │ ├── meanPow.m │ ├── meanProd.m │ ├── meanScale.m │ ├── meanSum.m │ └── meanZero.m ├── meanFunctions.m ├── penalized_gp.m ├── startup.m └── util │ ├── binaryEPGP.m │ ├── binaryGP.m │ ├── binaryLaplaceGP.m │ ├── brentmin.m │ ├── elsympol.m │ ├── elsympol2.m │ ├── gpr.m │ ├── lbfgsb.m │ ├── lbfgsb │ ├── Makefile │ ├── README.html │ ├── array.h │ ├── arrayofmatrices.cpp │ ├── arrayofmatrices.h │ ├── lbfgsb.cpp │ ├── license.txt │ ├── matlabexception.cpp │ ├── matlabexception.h │ ├── matlabmatrix.cpp │ ├── matlabmatrix.h │ ├── matlabprogram.cpp │ ├── matlabprogram.h │ ├── matlabscalar.cpp │ ├── matlabscalar.h │ ├── matlabstring.cpp │ ├── matlabstring.h │ ├── program.cpp │ ├── program.h │ └── solver.f │ ├── make.m │ ├── minimize.m │ ├── minimize_bfgs.m │ ├── minimize_lbfgsb.m │ ├── minimize_lbfgsb_gradfun.m │ ├── minimize_lbfgsb_objfun.m │ ├── minimize_may18.m │ ├── minimize_may21.m │ ├── minimize_pre_oct26.m │ ├── old_minimize.m │ ├── rewrap.m │ ├── solve_chol.c │ ├── solve_chol.m │ ├── sq_dist.m │ └── unwrap.m ├── methods ├── common_gp_parameters.m ├── fail_model.m ├── gp_add.m ├── gp_add_class_lo.m ├── gp_add_class_lo_1.m ├── gp_add_general_lo.m ├── gp_add_lo.m ├── gp_add_lo_1.m ├── gp_ard.m ├── gp_ard_class.m ├── gp_ard_general.m ├── hkl │ ├── add_one_source_c.c │ ├── add_one_source_c.mexa64 │ ├── center_gram_matrix.m │ ├── center_logistic.m │ ├── compile_hkl.m │ ├── compute_cubic_spline_kernel.m │ ├── compute_hull_general.m │ ├── compute_hull_withinhull.m │ ├── compute_sources.m │ ├── demo_classification.m │ ├── demo_regression.m │ ├── demo_regression_kfold.m │ ├── devectorize_single.c │ ├── devectorize_single.mexa64 │ ├── find_existing_source_transpose.c │ ├── find_existing_source_transpose.mexa64 │ ├── find_existing_source_transpose_min.c │ ├── find_existing_source_transpose_min.mexa64 │ ├── find_sources_complement_grid_fast_int_all_active_c.c │ ├── find_sources_complement_grid_fast_int_all_active_c.mexa64 │ ├── find_sources_complement_grid_fast_int_c.c │ ├── find_sources_complement_grid_fast_int_c.mexa64 │ ├── get_X_cell_efficient.m │ ├── get_data_reduced.m │ ├── get_kernel_data.m │ ├── get_reduced_graph_weights_sources.m │ ├── hermite_polynomials.m │ ├── hkl.m │ ├── hkl_3_0_documentation.txt │ ├── hkl_classification.m │ ├── hkl_kfold.m │ ├── hkl_regression.m │ ├── hkl_test.m │ ├── icd_general.c │ ├── icd_general.mexa64 │ ├── ind2subv.c │ ├── ind2subv.mexa64 │ ├── logistic_cost.m │ ├── logistic_cost_dual.m │ ├── minimize_newton.m │ ├── predict_test.m │ ├── predict_train_test.m │ ├── predict_train_test_unreg.m │ ├── simplex_projection.m │ ├── solve_hkl.m │ ├── solve_hkl_logistic_dual_fast.m │ ├── solve_hkl_logistic_dual_fast_kernels.m │ ├── solve_hkl_square_dual_fast.m │ ├── solve_hkl_square_dual_fast_kernels.m │ ├── sqdist.m │ ├── study_hull_sources.m │ ├── symmetric_vectorize_single.c │ ├── symmetric_vectorize_single.mexa64 │ ├── temphull.mat │ ├── update_reduced_graph_weights_sources.m │ ├── update_sources.m │ ├── vectorize_quad_single.c │ └── vectorize_quad_single.mexa64 ├── lin_model.m └── logistic.m ├── misc ├── add_gp_SEiso.m ├── add_gp_periodic.m ├── add_gp_spline.m ├── check_grads.m ├── hypers_to_latex3.m ├── list_missing.m ├── nips2011_fold_results.mat ├── nips2011_raw_results.mat ├── print_hyperparameter_tables.m ├── print_hyperparameter_tables_lo.m ├── print_order_table.m ├── real_censored_test.m ├── real_data_playing.m ├── resultsToBargraph.m ├── resultsToLatex4.m ├── save_folds.m ├── sort_additive_hypers.m ├── sort_additive_hypers_lo.m ├── sort_additive_hypers_vo.m ├── synthetic_2nd_order_censored.m └── test_sympol.m ├── scripts ├── example.sh ├── print_all.sh ├── run_one_job.sh ├── submit_all.sh └── submit_one.sh └── utils ├── DEFAULT.m ├── argmin.m ├── barweb.m ├── check_grad.m ├── checkgrad.m ├── exp10.m ├── fixMatrix.m ├── gen_kfolds.m ├── hline.m ├── ind2subv.m ├── latex_safe_str.m ├── license.txt ├── logsumexp.m ├── nanmean.m ├── print_dataset_stats.m ├── print_table.m ├── resultsToLatexEB.m ├── save2pdf.m ├── set_pagewidth.m ├── set_pagewidth2.m ├── set_thesis_fonts.m ├── sigmoid.m └── vline.m /.gitignore: -------------------------------------------------------------------------------- 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