├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── base_dir.m ├── demo ├── base_dir.m ├── demo_MPF.m ├── demo_all.m ├── demo_bwVK.m ├── demo_dich_gauss_01.m ├── demo_dich_gauss_bivar_bayes.m ├── demo_dich_gauss_counts.m ├── demo_dich_gauss_temporal_correlations.m ├── demo_flat_models.m ├── demo_iterscaling.m ├── demo_maxent.m ├── demo_maxent_MCMC.m ├── demo_maxent_counts.m ├── demo_simulation.m └── demo_vary_temperature.m ├── dich_gauss ├── DGAnyMarginal.m ├── DGPoisson.m ├── FindDGAnyMarginal.m ├── PoissonMarginals.m ├── SampleDGAnyMarginal.m ├── findLatentGaussian01.m ├── fit_flat_dg.m ├── fit_lowrank_dg.m ├── fit_semiflat_dg.m ├── sampleDichGauss01.m └── sampleDichGauss_tempCorrs.m ├── maxent ├── maxent_MCMC │ ├── MCMCbase │ │ ├── ApproxFinishLines.m │ │ ├── C_Code │ │ │ ├── OutputFunctions.c │ │ │ ├── OutputFunctions.h │ │ │ ├── OutputFunctions.o │ │ │ ├── ReadInputs.c │ │ │ ├── ReadInputs.h │ │ │ ├── ReadInputs.o │ │ │ ├── expec_err.c │ │ │ ├── expec_err.h │ │ │ ├── expec_err.o │ │ │ ├── fake_data.c │ │ │ ├── fake_data.exe │ │ │ ├── fake_data.o │ │ │ ├── learn_iterative.c │ │ │ ├── learn_iterative.h │ │ │ ├── learn_iterative.o │ │ │ ├── learn_stop.c │ │ │ ├── learn_stop.exe │ │ │ ├── learn_stop.h │ │ │ ├── learn_stop.o │ │ │ ├── learn_stopBU.c │ │ │ ├── makefile │ │ │ ├── mt19937ar.c │ │ │ ├── mt19937ar.h │ │ │ ├── mt19937ar.o │ │ │ ├── sampler.c │ │ │ ├── sampler.h │ │ │ ├── sampler.o │ │ │ ├── shuffle.c │ │ │ ├── shuffle.exe │ │ │ ├── shuffle.h │ │ │ └── shuffle.o │ │ ├── DispProgress.m │ │ ├── ReadResultDataFile.m │ │ ├── ReadTrackFile.m │ │ ├── SampleIsing.m │ │ ├── TrainIsing.m │ │ ├── WriteDataFile.m │ │ └── temp_files │ │ │ └── directory_for_temp_files │ ├── MCMCfast │ │ ├── GibbsLoop.m │ │ ├── MEX │ │ │ ├── pwGibbsMaxEnt_cluster.cpp │ │ │ ├── pwGibbsMaxEnt_cluster.mexa64 │ │ │ ├── pwGibbsMaxEnt_d30.cpp │ │ │ ├── pwGibbsMaxEnt_d30.mexw32 │ │ │ ├── pwGibbsMaxEnt_malloc.cpp │ │ │ ├── pwGibbsMaxEnt_malloc.mexw32 │ │ │ ├── pwGibbsMaxEnt_noRB.cpp │ │ │ └── pwGibbsMaxEnt_noRB.mexa64 │ │ ├── iterScaling.m │ │ ├── iterScalingAllVKs.m │ │ ├── maxEnt_features_slim.m │ │ ├── maxEnt_gibbs.m │ │ ├── maxEnt_gibbs_pair.m │ │ ├── maxEnt_gibbs_pair_C.m │ │ └── maxEnt_gibbs_pair_C_noRB.m │ └── setup_features_maxent.m ├── maxent_MPF │ ├── K_dK_ising_PK.m │ └── fit_maxent_mpf.m ├── maxent_exact │ ├── fit_ising_model.m │ ├── fit_maxent_linear.m │ ├── logPMaxEnt.m │ └── qIsing.m └── maxent_flat │ ├── fit_flat_ising_model.m │ ├── fit_flat_maxent_model.m │ ├── flat_model_vary_temperature.m │ └── sample_flat_model.m ├── startup.m ├── third_party └── minfunc_2012 │ ├── autoDif │ ├── autoGrad.m │ ├── autoHess.m │ ├── autoHv.m │ ├── autoTensor.m │ ├── derivativeCheck.m │ └── fastDerivativeCheck.m │ ├── example_derivativeCheck.m │ ├── example_minFunc.m │ ├── logisticExample │ ├── LogisticDiagPrecond.m │ ├── LogisticHv.m │ ├── LogisticLoss.m │ ├── example_minFunc_LR.m │ └── mylogsumexp.m │ ├── mexAll.m │ ├── minFunc │ ├── ArmijoBacktrack.m │ ├── WolfeLineSearch.m │ ├── conjGrad.m │ ├── dampedUpdate.m │ ├── isLegal.m │ ├── lbfgs.m │ ├── lbfgsAdd.m │ ├── lbfgsProd.m │ ├── lbfgsUpdate.m │ ├── mchol.m │ ├── mcholinc.m │ ├── minFunc.m │ ├── minFunc_processInputOptions.m │ ├── polyinterp.m │ ├── precondDiag.m │ ├── precondTriu.m │ ├── precondTriuDiag.m │ └── taylorModel.m │ └── minfunc │ ├── compiled │ ├── lbfgsAddC.mexa64 │ ├── lbfgsAddC.mexmaci64 │ ├── lbfgsAddC.mexw64 │ ├── lbfgsC.mexa64 │ ├── lbfgsC.mexglx │ ├── lbfgsC.mexmac │ ├── lbfgsC.mexmaci │ ├── lbfgsC.mexmaci64 │ ├── lbfgsC.mexw32 │ ├── lbfgsC.mexw64 │ ├── lbfgsProdC.mexa64 │ ├── lbfgsProdC.mexmaci64 │ ├── lbfgsProdC.mexw64 │ ├── mcholC.mexa64 │ ├── mcholC.mexglx │ ├── mcholC.mexmac │ ├── mcholC.mexmaci64 │ ├── mcholC.mexw32 │ └── mcholC.mexw64 │ └── mex │ ├── lbfgsAddC.c │ ├── lbfgsC.c │ ├── lbfgsProdC.c │ └── mcholC.c └── util ├── BinToDec.m ├── BinaryToDec.m ├── CalcIndep.m ├── CalcMarginals.m ├── CompZ.m ├── CountStates.m ├── DecToBin.m ├── DecToBinary.m ├── EstimateDiscreteJoint.m ├── FirstMoments.m ├── all_states.m ├── bivnor.c ├── bivnor.dll ├── bivnor.m ├── bivnor.mexa64 ├── bivnor.mexglx ├── bivnor.mexmaci ├── bivnor.mexmaci64 ├── calc_hankel_from_data.m ├── calc_mean_var.m ├── col_sum.m ├── corr_2_cov_01.m ├── countElem.m ├── count_distrib_2_ps.m ├── cov_2_corr.m ├── dich_gauss ├── Lambda_2_Rho.m ├── Lambda_2_Sigma.m ├── Rho_2_Lambda.m ├── dich_gauss_bivar_bayes │ ├── ProbDist.m │ ├── ProbDist2D.m │ ├── bivbern_fit.m │ ├── bivbern_lik.m │ ├── bivbern_lut.m │ └── count_events.m └── dich_gauss_probs.m ├── ent.m ├── eqline.m ├── getDataMomentsFromPKforFullModel.m ├── getEfxFromData.m ├── hJ2lambda.m ├── higham.m ├── logsumexp.m ├── maxent_exact └── fit_maxent_linear_costfunction.m ├── maxent_flat ├── CalcProbsForFitting.m ├── entropy_flat_dg.m ├── entropy_flat_dg_asymp.m ├── entropy_flat_ising_asymp.m ├── entropy_flat_model.m ├── flat_dg_count_distrib.m ├── flat_dg_count_distrib_asymp.m ├── flat_ising_count_distrib.m ├── 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