├── .gitignore ├── LICENSE ├── README.md ├── example ├── 1_minimal_code_example.ipynb ├── 2_two_moons_example.ipynb ├── 3_slcp_example.ipynb ├── README.md └── utils.py ├── figures ├── fig1_2 │ ├── README.md │ ├── fig1a.pdf │ ├── fig1a.png │ ├── fig1a.svg │ ├── fig1b.pdf │ ├── fig1b.png │ ├── fig1b.svg │ └── model_illustration.svg ├── fig3_4 │ ├── README.md │ ├── all_cond_task.svg │ ├── all_cond_task_reduced_methods.svg │ ├── all_cond_task_vpsde.svg │ ├── base_fig.ipynb │ ├── fig3.ipynb │ ├── fig3.png │ ├── fig3.svg │ ├── fig4.ipynb │ ├── fig4.svg │ ├── fig4_appendix.svg │ ├── fig4_appendix_vpsde.svg │ ├── method_legend.svg │ ├── method_legend_reduced.svg │ ├── sbibm_task.svg │ ├── sbibm_task_reduced_methods.svg │ └── sbibm_task_vpsde.svg ├── fig5 │ ├── README.md │ ├── base_fig.ipynb │ ├── bm_lv.svg │ ├── bm_lv_posterior.svg │ ├── fig5.ipynb │ ├── fig5.pdf │ ├── fig5.png │ ├── fig5.svg │ ├── lv_few_observations.svg │ ├── lv_many_observations.svg │ └── method_legend.svg ├── fig6 │ ├── README.md │ ├── base_fig.ipynb │ ├── base_fig_old.ipynb │ ├── compute_cov.py │ ├── compute_cov.py:Zone.Identifier │ ├── compute_cov.sh │ ├── compute_cov.sh:Zone.Identifier │ ├── fig6.ipynb │ ├── fig6_new.png │ ├── fig6_new.svg │ ├── fig6_old.png │ ├── fig6_old.svg │ ├── log_probs_q.npy │ ├── log_probs_q.npy:Zone.Identifier │ ├── log_probs_q1.npy │ ├── log_probs_q1.npy:Zone.Identifier │ ├── log_probs_q_all_cond.npy │ ├── log_probs_q_all_cond.npy:Zone.Identifier │ ├── log_probs_q_all_cond1.npy │ ├── log_probs_q_all_cond1.npy:Zone.Identifier │ ├── log_probs_true.npy │ ├── log_probs_true.npy:Zone.Identifier │ ├── log_probs_true1.npy │ ├── log_probs_true1.npy:Zone.Identifier │ ├── log_probs_true_all_cond.npy │ ├── log_probs_true_all_cond.npy:Zone.Identifier │ ├── log_probs_true_all_cond1.npy │ ├── log_probs_true_all_cond1.npy:Zone.Identifier │ ├── sir_coverage_all_cond.svg │ ├── sir_coverage_posterior.svg │ ├── sir_example1.svg │ ├── sir_example1_new.svg │ ├── sir_example2.svg │ ├── sir_example2_new.svg │ ├── sir_example_emulation2.svg │ └── sir_example_emulation2_new.svg ├── fig7 │ ├── Hodgkin-Huxley.svg │ ├── README.md │ ├── base_fig.ipynb │ ├── bm_hh_marginal.pdf │ ├── bm_hh_marginal.svg │ ├── bm_hh_marginal_all_features.svg │ ├── bm_hh_marginal_energies_constrained.svg │ ├── bm_hh_marginal_energy.svg │ ├── bm_hh_marginal_energy_all_features.svg │ ├── bm_hh_marginal_energy_constraint.svg │ ├── bm_hh_traces.svg │ ├── bm_hh_traces_energy_constrained.svg │ ├── fig7.ipynb │ ├── fig7.svg │ ├── fig7_final.pdf │ ├── fig7_final.png │ ├── fig7_final.svg │ ├── illustration.svg │ ├── true_energy.svg │ └── true_trace.svg └── fig_appendix │ ├── bernoulli_glm │ ├── bernoulli_glm.ipynb │ ├── bernoulli_task.png │ └── bernoulli_task.svg │ ├── coverage │ ├── coverage_bm.ipynb │ ├── coverage_two_moons.ipynb │ ├── coverage_two_moons_100k.png │ ├── coverage_two_moons_100k.svg │ ├── coverage_two_moons_1k.png │ ├── coverage_two_moons_1k.svg │ ├── npe_expected_coverage.pdf │ ├── npe_expected_coverage.png │ ├── npe_expected_coverage.svg │ ├── npe_nle_expected_coverage.pdf │ ├── npe_nle_expected_coverage.png │ ├── npe_nle_expected_coverage.svg │ ├── simformer_directed_expected_coverage.pdf │ ├── simformer_directed_expected_coverage.png │ ├── simformer_directed_expected_coverage.svg │ ├── simformer_expected_coverage.pdf │ ├── simformer_expected_coverage.png │ ├── simformer_expected_coverage.svg │ ├── simformer_undirected_expected_coverage.pdf │ ├── simformer_undirected_expected_coverage.png │ └── simformer_undirected_expected_coverage.svg │ ├── gravitational_waves │ ├── ec_gw_full_post.svg │ ├── ec_gw_full_post.svg:Zone.Identifier │ ├── ec_gw_partial1_post.svg │ ├── ec_gw_partial1_post.svg:Zone.Identifier │ ├── ec_gw_partial2_post.svg │ ├── ec_gw_partial2_post.svg:Zone.Identifier │ ├── ec_gw_test.svg │ ├── ec_gw_test.svg:Zone.Identifier │ ├── gw_coverage1.py │ ├── gw_coverage1.py:Zone.Identifier │ ├── gw_coverage2.py │ ├── gw_coverage2.py:Zone.Identifier │ ├── gw_coverage3.py │ ├── gw_coverage3.py:Zone.Identifier │ ├── gw_ec_script.sh │ ├── gw_ec_script.sh:Zone.Identifier │ ├── gw_final_fig.pdf │ ├── gw_final_fig.pdf:Zone.Identifier │ ├── gw_final_fig.svg │ ├── gw_final_fig.svg:Zone.Identifier │ ├── job_output_371039.txt │ ├── job_output_371039.txt:Zone.Identifier │ ├── job_output_371042.txt │ ├── job_output_371042.txt:Zone.Identifier │ ├── job_output_371043.txt │ ├── job_output_371043.txt:Zone.Identifier │ ├── job_output_371626.txt │ ├── job_output_371626.txt:Zone.Identifier │ ├── job_output_371627.txt │ ├── job_output_371627.txt:Zone.Identifier │ ├── job_output_371628.txt │ ├── job_output_371628.txt:Zone.Identifier │ ├── log_probs_q_vec_full_posterior.npy │ ├── log_probs_q_vec_full_posterior.npy:Zone.Identifier │ ├── log_probs_q_vec_partial1_posterior.npy │ ├── log_probs_q_vec_partial1_posterior.npy:Zone.Identifier │ ├── log_probs_q_vec_partial2_posterior.npy │ ├── log_probs_q_vec_partial2_posterior.npy:Zone.Identifier │ ├── log_probs_q_vec_test.pt.npy │ ├── log_probs_q_vec_test.pt.npy:Zone.Identifier │ ├── log_probs_true_test.pt.npy │ ├── log_probs_true_test.pt.npy:Zone.Identifier │ ├── log_probs_true_vec_full_posterior.npy │ ├── log_probs_true_vec_full_posterior.npy:Zone.Identifier │ ├── log_probs_true_vec_partial1_posterior.npy │ ├── log_probs_true_vec_partial1_posterior.npy:Zone.Identifier │ ├── log_probs_true_vec_partial2_posterior.npy │ ├── log_probs_true_vec_partial2_posterior.npy:Zone.Identifier │ ├── only_post_params.pt.npy │ ├── only_post_params.pt.npy:Zone.Identifier │ ├── posteriors_obsevation5000.svg │ ├── posteriors_obsevation5000.svg:Zone.Identifier │ ├── posteriors_obsevation6000.svg │ ├── posteriors_obsevation6000.svg:Zone.Identifier │ ├── posteriors_obsevation7300.svg │ ├── posteriors_obsevation7300.svg:Zone.Identifier │ ├── posteriors_obsevation9001.svg │ ├── posteriors_obsevation9001.svg:Zone.Identifier │ ├── sbiscore_gravittaional_waves_only_post.ipynb │ └── sbiscore_gravittaional_waves_only_post.ipynb:Zone.Identifier │ ├── guidance_results │ ├── abstract_guidance_two_moons_example.svg │ ├── fig2_appendix.ipynb │ ├── fig2_appendix.svg │ ├── fig3_appendix.pdf │ ├── guidance_bm.ipynb │ ├── guidance_example.ipynb │ └── guidance_two_moons_example.svg │ ├── masks │ ├── mask1.svg │ ├── mask1.svg:Zone.Identifier │ ├── mask2.svg │ ├── mask2.svg:Zone.Identifier │ ├── mask3.svg │ ├── mask3.svg:Zone.Identifier │ ├── mask4.svg │ ├── mask4.svg:Zone.Identifier │ ├── mask5.svg │ ├── mask5.svg:Zone.Identifier │ ├── mask6.svg │ ├── mask6.svg:Zone.Identifier │ ├── masks_fig.ipynb │ └── masks_fig.ipynb:Zone.Identifier │ ├── nlls │ ├── log_prob_time_steps.png │ ├── log_prob_time_steps.svg │ ├── nll_posterior.pdf │ ├── nll_posterior.svg │ ├── nlls.ipynb │ └── nlls_speed.ipynb │ ├── time_steps │ ├── figs.ipynb │ └── time_steps.svg │ └── toy_illustrations │ ├── correct_joint_estimation_with_correct_marginals.svg │ ├── correct_joint_estimation_without_correct_marginals.svg │ ├── correct_marginal_estimation.pdf │ ├── correct_marginal_estimation.svg │ ├── directed_likelihood_mask_hmm.svg │ ├── directed_posterior_mask_hmm.svg │ ├── fig1_appendix.pdf │ ├── fig1_appendix.svg │ ├── fig_appendix1.ipynb │ ├── graphical_structure.ipynb │ ├── hmm_mask_per_layer.pdf │ ├── hmm_mask_per_layer.svg │ ├── incorrect_and_correct_marginal_estimation.pdf │ ├── incorrect_and_correct_marginal_estimation.svg │ ├── incorrect_marginal_estimation.pdf │ ├── incorrect_marginal_estimation.svg │ ├── scoresbi_constraint_conditioning.png │ ├── scoresbi_constraint_conditioning.svg │ ├── scoresbi_likelihood_change.png │ ├── scoresbi_likelihood_change.svg │ ├── scoresbi_likelihood_change2.svg │ ├── scoresbi_playground_vesde.ipynb │ ├── scoresbi_playground_vesde_without_marginalization.ipynb │ ├── scoresbi_prior_change.svg │ ├── scoresbi_prior_change2.svg │ ├── scoresbi_theta1.png │ ├── scoresbi_theta_full_posterior.png │ └── scoresbi_theta_x1.png ├── results └── example_guidance │ ├── models │ ├── model_0.pkl │ ├── model_1.pkl │ └── model_2.pkl │ └── summary.csv └── src ├── environment.yml ├── probjax ├── README.md ├── probjax │ ├── __init__.py │ ├── core │ │ ├── __init__.py │ │ ├── custom_primitives │ │ │ ├── __init__.py │ │ │ ├── custom_inverse.py │ │ │ └── random_variable.py │ │ ├── interpreters │ │ │ ├── constraints.py │ │ │ ├── interventions.py │ │ │ ├── inverse.py │ │ │ ├── joint_sample.py │ │ │ ├── log_potential.py │ │ │ └── trace.py │ │ ├── jaxpr_propagation │ │ │ ├── graph.py │ │ │ ├── interpret.py │ │ │ ├── propagate.py │ │ │ └── utils.py │ │ └── transformation.py │ ├── distributions │ │ ├── __init__.py │ │ ├── constraint_registry.py │ │ ├── constraints.py │ │ ├── continuous.py │ │ ├── discrete.py │ │ ├── distribution.py │ │ ├── divergences │ │ │ ├── __init__.py │ │ │ ├── divergence.py │ │ │ ├── kl.py │ │ │ └── wasserstein.py │ │ ├── exponential_family.py │ │ ├── independent.py │ │ ├── mixture.py │ │ ├── sde.py │ │ ├── transformed_distribution.py │ │ ├── truncated_distribution.py │ │ └── utils.py │ ├── inference │ │ ├── __init__.py │ │ ├── kalman_filter.py │ │ ├── marcov_kernels.py │ │ ├── mcmc.py │ │ ├── rejection.py │ │ ├── smc.py │ │ └── states.py │ ├── nn │ │ ├── __init__.py │ │ ├── attention.py │ │ ├── autoregressive.py │ │ ├── bijective.py │ │ ├── coupling.py │ │ ├── helpers.py │ │ ├── loss_fn.py │ │ ├── tokenizer.py │ │ ├── transformers.py │ │ └── unets.py │ └── utils │ │ ├── __init__.py │ │ ├── brownian.py │ │ ├── containers.py │ │ ├── graph.py │ │ ├── interpolation.py │ │ ├── jaxutils.py │ │ ├── linalg.py │ │ ├── odeint.py │ │ ├── sdeint.py │ │ ├── solver.py │ │ ├── stats.py │ │ └── torchvision_datasets.py ├── setup.py └── tests │ ├── config_flows.py │ ├── conftest.py │ ├── test_core_inverse_and_log_det.py │ ├── test_distributions.py │ ├── test_distributions_constraints.py │ ├── test_flows.py │ ├── test_nn.py │ ├── test_odeint.py │ └── test_sdeint.py ├── requirements.txt └── scoresbibm ├── README.md ├── config ├── __init__.py ├── config.yaml ├── eval │ ├── all.yaml │ ├── c2st.yaml │ ├── c2st_all_posterior.yaml │ ├── c2st_joint.yaml │ ├── c2st_posterior.yaml │ ├── cov.yaml │ ├── cov_likelihood.yaml │ ├── cov_likelihood_fast.yaml │ ├── cov_posterior.yaml │ ├── metric │ │ ├── c2st.yaml │ │ ├── c2st_joint.yaml │ │ ├── c2st_likelihood.yaml │ │ ├── c2st_posterior.yaml │ │ ├── c2st_random.yaml │ │ ├── condition_mask_fn │ │ │ ├── joint.yaml │ │ │ ├── likelihood.yaml │ │ │ ├── posterior.yaml │ │ │ ├── random.yaml │ │ │ └── structured_random.yaml │ │ ├── cov_likelihood.yaml │ │ ├── cov_likelihood_fast.yaml │ │ ├── cov_posterior.yaml │ │ ├── mmd.yaml │ │ ├── nll_joint.yaml │ │ ├── nll_likelihood.yaml │ │ ├── nll_posterior.yaml │ │ └── none.yaml │ ├── nll.yaml │ ├── nll_cov.yaml │ ├── nll_cov_likelihood.yaml │ ├── nll_cov_posterior.yaml │ ├── nll_joint.yaml │ ├── nll_likelihood.yaml │ ├── nll_posterior.yaml │ └── none.yaml ├── experiment │ ├── bm.yaml │ ├── bm_additional.yaml │ ├── bm_additional_nle.yaml │ ├── bm_additional_npe.yaml │ ├── bm_all_cond.yaml │ ├── bm_all_cond_joint.yaml │ ├── bm_all_cond_joint_eval.yaml │ ├── bm_base.yaml │ ├── bm_hh.yaml │ ├── bm_lv.yaml │ ├── bm_lv_eval1.yaml │ ├── bm_lv_eval2.yaml │ ├── bm_lv_eval3.yaml │ ├── bm_score_base.yaml │ ├── bm_sir.yaml │ ├── bm_sir_new.yaml │ ├── bm_time_steps.yaml │ ├── bm_time_steps_eval.yaml │ └── example_all_cond.yaml ├── launcher │ ├── local.yaml │ └── slurm.yaml ├── method │ ├── model │ │ ├── classifier_nn.yaml │ │ ├── likelihood_nn.yaml │ │ ├── posterior_nn.yaml │ │ ├── score_mlp.yaml │ │ ├── score_transformer.yaml │ │ ├── score_transformer_large.yaml │ │ ├── score_transformer_large_token.yaml │ │ ├── score_transformer_small.yaml │ │ └── score_transformer_unconditional.yaml │ ├── nle.yaml │ ├── npe.yaml │ ├── nre.yaml │ ├── nspe.yaml │ ├── posterior │ │ ├── backward_ode.yaml │ │ ├── backward_sde.yaml │ │ ├── generalized_guidance.yaml │ │ ├── none.yaml │ │ ├── repaint_sde.yaml │ │ ├── slice_multi_chain_sbi.yaml │ │ └── slice_sbi.yaml │ ├── score_transformer.yaml │ ├── score_transformer_directed.yaml │ ├── score_transformer_joint.yaml │ ├── score_transformer_joint_undirected.yaml │ ├── score_transformer_posterior.yaml │ ├── score_transformer_undirected.yaml │ ├── sde │ │ ├── vesde.yaml │ │ └── vpsde.yaml │ └── train │ │ ├── condition_mask_fn │ │ ├── joint.yaml │ │ ├── likelihood.yaml │ │ ├── posterior.yaml │ │ ├── random.yaml │ │ └── structured_random.yaml │ │ ├── edge_mask_fn │ │ ├── faithfull.yaml │ │ ├── min_faithfull.yaml │ │ ├── none.yaml │ │ └── undirected.yaml │ │ ├── train_sbi.yaml │ │ ├── train_score_mlp.yaml │ │ └── train_score_transformer.yaml ├── partition │ ├── cpu.yaml │ ├── cpu_long.yaml │ ├── cpu_short.yaml │ ├── gpu.yaml │ ├── gpu_long.yaml │ ├── none.yaml │ └── v100.yaml ├── sweeper │ ├── grid.yaml │ ├── none.yaml │ ├── nsga2_mo.yaml │ ├── random.yaml │ ├── tpe.yaml │ └── tpe_mo.yaml └── task │ ├── bernoulli_glm.yaml │ ├── bernoulli_glm_raw.yaml │ ├── gaussian_linear.yaml │ ├── gaussian_mixture.yaml │ ├── hh.yaml │ ├── lotka_volterra.yaml │ ├── marcov_chain_all_cond.yaml │ ├── sir.yaml │ ├── slcp.yaml │ ├── slcp_all_cond.yaml │ ├── tree_all_cond.yaml │ ├── two_moons.yaml │ └── two_moons_all_cond.yaml ├── scoresbibm ├── evaluation │ ├── __init__.py │ ├── eval_metrics.py │ └── eval_task.py ├── methods │ ├── __init__.py │ ├── guidance.py │ ├── method_base.py │ ├── models.py │ ├── neural_nets.py │ ├── score_sbi.py │ ├── score_transformer.py │ └── sde.py ├── scripts │ ├── __init__.py │ └── hydra_script.py ├── tasks │ ├── __init__.py │ ├── all_conditional_tasks.py │ ├── base_task.py │ ├── hhtask.py │ ├── sbibm_tasks.py │ └── unstructured_tasks.py └── utils │ ├── __init__.py │ ├── condition_masks.py │ ├── data_utils.py │ ├── edge_masks.py │ ├── plot.py │ └── pyloric.mplstyle └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/README.md -------------------------------------------------------------------------------- /example/1_minimal_code_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/example/1_minimal_code_example.ipynb -------------------------------------------------------------------------------- /example/2_two_moons_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/example/2_two_moons_example.ipynb -------------------------------------------------------------------------------- /example/3_slcp_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/example/3_slcp_example.ipynb -------------------------------------------------------------------------------- /example/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/example/README.md -------------------------------------------------------------------------------- /example/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/example/utils.py -------------------------------------------------------------------------------- /figures/fig1_2/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/README.md -------------------------------------------------------------------------------- /figures/fig1_2/fig1a.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1a.pdf -------------------------------------------------------------------------------- /figures/fig1_2/fig1a.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1a.png -------------------------------------------------------------------------------- /figures/fig1_2/fig1a.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1a.svg -------------------------------------------------------------------------------- /figures/fig1_2/fig1b.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1b.pdf -------------------------------------------------------------------------------- /figures/fig1_2/fig1b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1b.png -------------------------------------------------------------------------------- /figures/fig1_2/fig1b.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/fig1b.svg -------------------------------------------------------------------------------- /figures/fig1_2/model_illustration.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig1_2/model_illustration.svg -------------------------------------------------------------------------------- /figures/fig3_4/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/README.md -------------------------------------------------------------------------------- /figures/fig3_4/all_cond_task.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/all_cond_task.svg -------------------------------------------------------------------------------- /figures/fig3_4/all_cond_task_reduced_methods.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/all_cond_task_reduced_methods.svg -------------------------------------------------------------------------------- /figures/fig3_4/all_cond_task_vpsde.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/all_cond_task_vpsde.svg -------------------------------------------------------------------------------- /figures/fig3_4/base_fig.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/base_fig.ipynb -------------------------------------------------------------------------------- /figures/fig3_4/fig3.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig3.ipynb -------------------------------------------------------------------------------- /figures/fig3_4/fig3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig3.png -------------------------------------------------------------------------------- /figures/fig3_4/fig3.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig3.svg -------------------------------------------------------------------------------- /figures/fig3_4/fig4.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig4.ipynb -------------------------------------------------------------------------------- /figures/fig3_4/fig4.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig4.svg -------------------------------------------------------------------------------- /figures/fig3_4/fig4_appendix.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig4_appendix.svg -------------------------------------------------------------------------------- /figures/fig3_4/fig4_appendix_vpsde.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/fig4_appendix_vpsde.svg -------------------------------------------------------------------------------- /figures/fig3_4/method_legend.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/method_legend.svg -------------------------------------------------------------------------------- /figures/fig3_4/method_legend_reduced.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/method_legend_reduced.svg -------------------------------------------------------------------------------- /figures/fig3_4/sbibm_task.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/sbibm_task.svg -------------------------------------------------------------------------------- /figures/fig3_4/sbibm_task_reduced_methods.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/sbibm_task_reduced_methods.svg -------------------------------------------------------------------------------- /figures/fig3_4/sbibm_task_vpsde.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig3_4/sbibm_task_vpsde.svg -------------------------------------------------------------------------------- /figures/fig5/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/README.md -------------------------------------------------------------------------------- /figures/fig5/base_fig.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/base_fig.ipynb -------------------------------------------------------------------------------- /figures/fig5/bm_lv.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/bm_lv.svg -------------------------------------------------------------------------------- /figures/fig5/bm_lv_posterior.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/bm_lv_posterior.svg -------------------------------------------------------------------------------- /figures/fig5/fig5.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/fig5.ipynb -------------------------------------------------------------------------------- /figures/fig5/fig5.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/fig5.pdf -------------------------------------------------------------------------------- /figures/fig5/fig5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/fig5.png -------------------------------------------------------------------------------- /figures/fig5/fig5.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/fig5.svg -------------------------------------------------------------------------------- /figures/fig5/lv_few_observations.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/lv_few_observations.svg -------------------------------------------------------------------------------- /figures/fig5/lv_many_observations.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/lv_many_observations.svg -------------------------------------------------------------------------------- /figures/fig5/method_legend.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig5/method_legend.svg -------------------------------------------------------------------------------- /figures/fig6/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/README.md -------------------------------------------------------------------------------- /figures/fig6/base_fig.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/base_fig.ipynb -------------------------------------------------------------------------------- /figures/fig6/base_fig_old.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/base_fig_old.ipynb -------------------------------------------------------------------------------- /figures/fig6/compute_cov.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/compute_cov.py -------------------------------------------------------------------------------- /figures/fig6/compute_cov.py:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/compute_cov.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/compute_cov.sh -------------------------------------------------------------------------------- /figures/fig6/compute_cov.sh:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/fig6.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/fig6.ipynb -------------------------------------------------------------------------------- /figures/fig6/fig6_new.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/fig6_new.png -------------------------------------------------------------------------------- /figures/fig6/fig6_new.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/fig6_new.svg -------------------------------------------------------------------------------- /figures/fig6/fig6_old.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/fig6_old.png -------------------------------------------------------------------------------- /figures/fig6/fig6_old.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/fig6_old.svg -------------------------------------------------------------------------------- /figures/fig6/log_probs_q.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_q.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_q.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_q1.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_q1.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_q1.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_q_all_cond.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_q_all_cond.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_q_all_cond.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_q_all_cond1.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_q_all_cond1.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_q_all_cond1.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_true.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_true.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_true.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_true1.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_true1.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_true1.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_true_all_cond.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_true_all_cond.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_true_all_cond.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/log_probs_true_all_cond1.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/log_probs_true_all_cond1.npy -------------------------------------------------------------------------------- /figures/fig6/log_probs_true_all_cond1.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig6/sir_coverage_all_cond.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_coverage_all_cond.svg -------------------------------------------------------------------------------- /figures/fig6/sir_coverage_posterior.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_coverage_posterior.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example1.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example1_new.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example1_new.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example2.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example2_new.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example2_new.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example_emulation2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example_emulation2.svg -------------------------------------------------------------------------------- /figures/fig6/sir_example_emulation2_new.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig6/sir_example_emulation2_new.svg -------------------------------------------------------------------------------- /figures/fig7/Hodgkin-Huxley.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/Hodgkin-Huxley.svg -------------------------------------------------------------------------------- /figures/fig7/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/README.md -------------------------------------------------------------------------------- /figures/fig7/base_fig.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/base_fig.ipynb -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal.pdf -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal_all_features.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal_all_features.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal_energies_constrained.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal_energies_constrained.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal_energy.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal_energy.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal_energy_all_features.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal_energy_all_features.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_marginal_energy_constraint.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_marginal_energy_constraint.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_traces.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_traces.svg -------------------------------------------------------------------------------- /figures/fig7/bm_hh_traces_energy_constrained.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/bm_hh_traces_energy_constrained.svg -------------------------------------------------------------------------------- /figures/fig7/fig7.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/fig7.ipynb -------------------------------------------------------------------------------- /figures/fig7/fig7.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/fig7.svg -------------------------------------------------------------------------------- /figures/fig7/fig7_final.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/fig7_final.pdf -------------------------------------------------------------------------------- /figures/fig7/fig7_final.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/fig7_final.png -------------------------------------------------------------------------------- /figures/fig7/fig7_final.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/fig7_final.svg -------------------------------------------------------------------------------- /figures/fig7/illustration.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/illustration.svg -------------------------------------------------------------------------------- /figures/fig7/true_energy.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/true_energy.svg -------------------------------------------------------------------------------- /figures/fig7/true_trace.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig7/true_trace.svg -------------------------------------------------------------------------------- /figures/fig_appendix/bernoulli_glm/bernoulli_glm.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/bernoulli_glm/bernoulli_glm.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/bernoulli_glm/bernoulli_task.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/bernoulli_glm/bernoulli_task.png -------------------------------------------------------------------------------- /figures/fig_appendix/bernoulli_glm/bernoulli_task.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/bernoulli_glm/bernoulli_task.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_bm.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_bm.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_two_moons.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_two_moons.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_two_moons_100k.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_two_moons_100k.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_two_moons_100k.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_two_moons_100k.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_two_moons_1k.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_two_moons_1k.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/coverage_two_moons_1k.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/coverage_two_moons_1k.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_expected_coverage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_expected_coverage.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_expected_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_expected_coverage.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_expected_coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_expected_coverage.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_nle_expected_coverage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_nle_expected_coverage.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_nle_expected_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_nle_expected_coverage.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/npe_nle_expected_coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/npe_nle_expected_coverage.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_directed_expected_coverage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_directed_expected_coverage.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_directed_expected_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_directed_expected_coverage.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_directed_expected_coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_directed_expected_coverage.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_expected_coverage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_expected_coverage.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_expected_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_expected_coverage.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_expected_coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_expected_coverage.svg -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_undirected_expected_coverage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_undirected_expected_coverage.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_undirected_expected_coverage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_undirected_expected_coverage.png -------------------------------------------------------------------------------- /figures/fig_appendix/coverage/simformer_undirected_expected_coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/coverage/simformer_undirected_expected_coverage.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_full_post.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/ec_gw_full_post.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_full_post.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_partial1_post.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/ec_gw_partial1_post.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_partial1_post.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_partial2_post.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/ec_gw_partial2_post.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_partial2_post.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_test.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/ec_gw_test.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/ec_gw_test.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_coverage1.py -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage1.py:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_coverage2.py -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage2.py:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_coverage3.py -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_coverage3.py:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_ec_script.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_ec_script.sh -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_ec_script.sh:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_final_fig.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_final_fig.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_final_fig.pdf:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_final_fig.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/gw_final_fig.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/gw_final_fig.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371039.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371039.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371039.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371042.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371042.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371042.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371043.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371043.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371043.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371626.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371626.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371626.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371627.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371627.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371627.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371628.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/job_output_371628.txt -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/job_output_371628.txt:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_full_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_q_vec_full_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_full_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial1_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial1_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial1_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial2_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial2_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_partial2_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_test.pt.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_q_vec_test.pt.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_q_vec_test.pt.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_test.pt.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_true_test.pt.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_test.pt.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_full_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_true_vec_full_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_full_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial1_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial1_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial1_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial2_posterior.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial2_posterior.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/log_probs_true_vec_partial2_posterior.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/only_post_params.pt.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/only_post_params.pt.npy -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/only_post_params.pt.npy:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation5000.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/posteriors_obsevation5000.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation5000.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation6000.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/posteriors_obsevation6000.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation6000.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation7300.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/posteriors_obsevation7300.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation7300.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation9001.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/posteriors_obsevation9001.svg -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/posteriors_obsevation9001.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/sbiscore_gravittaional_waves_only_post.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/gravitational_waves/sbiscore_gravittaional_waves_only_post.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/gravitational_waves/sbiscore_gravittaional_waves_only_post.ipynb:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/abstract_guidance_two_moons_example.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/abstract_guidance_two_moons_example.svg -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/fig2_appendix.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/fig2_appendix.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/fig2_appendix.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/fig2_appendix.svg -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/fig3_appendix.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/fig3_appendix.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/guidance_bm.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/guidance_bm.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/guidance_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/guidance_example.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/guidance_results/guidance_two_moons_example.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/guidance_results/guidance_two_moons_example.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask1.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask1.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask2.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask2.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask3.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask3.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask3.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask4.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask4.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask4.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask5.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask5.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask5.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask6.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/mask6.svg -------------------------------------------------------------------------------- /figures/fig_appendix/masks/mask6.svg:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/masks/masks_fig.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/masks/masks_fig.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/masks/masks_fig.ipynb:Zone.Identifier: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/log_prob_time_steps.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/log_prob_time_steps.png -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/log_prob_time_steps.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/log_prob_time_steps.svg -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/nll_posterior.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/nll_posterior.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/nll_posterior.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/nll_posterior.svg -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/nlls.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/nlls.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/nlls/nlls_speed.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/nlls/nlls_speed.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/time_steps/figs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/time_steps/figs.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/time_steps/time_steps.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/time_steps/time_steps.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/correct_joint_estimation_with_correct_marginals.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/correct_joint_estimation_with_correct_marginals.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/correct_joint_estimation_without_correct_marginals.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/correct_joint_estimation_without_correct_marginals.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/correct_marginal_estimation.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/correct_marginal_estimation.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/correct_marginal_estimation.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/correct_marginal_estimation.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/directed_likelihood_mask_hmm.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/directed_likelihood_mask_hmm.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/directed_posterior_mask_hmm.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/directed_posterior_mask_hmm.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/fig1_appendix.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/fig1_appendix.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/fig1_appendix.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/fig1_appendix.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/fig_appendix1.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/fig_appendix1.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/graphical_structure.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/graphical_structure.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/hmm_mask_per_layer.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/hmm_mask_per_layer.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/hmm_mask_per_layer.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/hmm_mask_per_layer.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/incorrect_and_correct_marginal_estimation.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/incorrect_and_correct_marginal_estimation.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/incorrect_and_correct_marginal_estimation.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/incorrect_and_correct_marginal_estimation.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/incorrect_marginal_estimation.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/incorrect_marginal_estimation.pdf -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/incorrect_marginal_estimation.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/incorrect_marginal_estimation.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_constraint_conditioning.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_constraint_conditioning.png -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_constraint_conditioning.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_constraint_conditioning.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change.png -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_likelihood_change2.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_playground_vesde.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_playground_vesde.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_playground_vesde_without_marginalization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_playground_vesde_without_marginalization.ipynb -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_prior_change.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_prior_change.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_prior_change2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_prior_change2.svg -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_theta1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_theta1.png -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_theta_full_posterior.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_theta_full_posterior.png -------------------------------------------------------------------------------- /figures/fig_appendix/toy_illustrations/scoresbi_theta_x1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/figures/fig_appendix/toy_illustrations/scoresbi_theta_x1.png -------------------------------------------------------------------------------- /results/example_guidance/models/model_0.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/results/example_guidance/models/model_0.pkl -------------------------------------------------------------------------------- /results/example_guidance/models/model_1.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/results/example_guidance/models/model_1.pkl -------------------------------------------------------------------------------- /results/example_guidance/models/model_2.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/results/example_guidance/models/model_2.pkl -------------------------------------------------------------------------------- /results/example_guidance/summary.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/results/example_guidance/summary.csv -------------------------------------------------------------------------------- /src/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/environment.yml -------------------------------------------------------------------------------- /src/probjax/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/README.md -------------------------------------------------------------------------------- /src/probjax/probjax/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/probjax/probjax/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/__init__.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/custom_primitives/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/probjax/probjax/core/custom_primitives/custom_inverse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/custom_primitives/custom_inverse.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/custom_primitives/random_variable.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/custom_primitives/random_variable.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/constraints.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/constraints.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/interventions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/interventions.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/inverse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/inverse.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/joint_sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/joint_sample.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/log_potential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/log_potential.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/interpreters/trace.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/interpreters/trace.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/jaxpr_propagation/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/jaxpr_propagation/graph.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/jaxpr_propagation/interpret.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/jaxpr_propagation/interpret.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/jaxpr_propagation/propagate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/jaxpr_propagation/propagate.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/jaxpr_propagation/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/jaxpr_propagation/utils.py -------------------------------------------------------------------------------- /src/probjax/probjax/core/transformation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/core/transformation.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/__init__.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/constraint_registry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/constraint_registry.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/constraints.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/constraints.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/continuous.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/continuous.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/discrete.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/discrete.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/distribution.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/divergences/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/divergences/__init__.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/divergences/divergence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/divergences/divergence.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/divergences/kl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/divergences/kl.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/divergences/wasserstein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/divergences/wasserstein.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/exponential_family.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/exponential_family.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/independent.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/independent.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/mixture.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/mixture.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/sde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/sde.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/transformed_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/transformed_distribution.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/truncated_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/truncated_distribution.py -------------------------------------------------------------------------------- /src/probjax/probjax/distributions/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/distributions/utils.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/probjax/probjax/inference/kalman_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/kalman_filter.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/marcov_kernels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/marcov_kernels.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/mcmc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/mcmc.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/rejection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/rejection.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/smc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/smc.py -------------------------------------------------------------------------------- /src/probjax/probjax/inference/states.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/inference/states.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/__init__.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/attention.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/autoregressive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/autoregressive.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/bijective.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/bijective.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/coupling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/coupling.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/helpers.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/loss_fn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/loss_fn.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/tokenizer.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/transformers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/transformers.py -------------------------------------------------------------------------------- /src/probjax/probjax/nn/unets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/nn/unets.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | import random -------------------------------------------------------------------------------- /src/probjax/probjax/utils/brownian.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/brownian.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/containers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/containers.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/graph.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/interpolation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/interpolation.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/jaxutils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/jaxutils.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/linalg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/linalg.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/odeint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/odeint.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/sdeint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/sdeint.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/solver.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/solver.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/stats.py -------------------------------------------------------------------------------- /src/probjax/probjax/utils/torchvision_datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/probjax/utils/torchvision_datasets.py -------------------------------------------------------------------------------- /src/probjax/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/setup.py -------------------------------------------------------------------------------- /src/probjax/tests/config_flows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/config_flows.py -------------------------------------------------------------------------------- /src/probjax/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/conftest.py -------------------------------------------------------------------------------- /src/probjax/tests/test_core_inverse_and_log_det.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/test_core_inverse_and_log_det.py -------------------------------------------------------------------------------- /src/probjax/tests/test_distributions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/test_distributions.py -------------------------------------------------------------------------------- /src/probjax/tests/test_distributions_constraints.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/probjax/tests/test_flows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/test_flows.py -------------------------------------------------------------------------------- /src/probjax/tests/test_nn.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/probjax/tests/test_odeint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/test_odeint.py -------------------------------------------------------------------------------- /src/probjax/tests/test_sdeint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/probjax/tests/test_sdeint.py -------------------------------------------------------------------------------- /src/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/requirements.txt -------------------------------------------------------------------------------- /src/scoresbibm/README.md: -------------------------------------------------------------------------------- 1 | 2 | ## Scoresbibm 3 | 4 | -------------------------------------------------------------------------------- /src/scoresbibm/config/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/scoresbibm/config/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/config.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/all.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/all.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/c2st.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/c2st.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/c2st_all_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/c2st_all_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/c2st_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/c2st_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/c2st_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/c2st_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/cov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/cov.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/cov_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/cov_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/cov_likelihood_fast.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/cov_likelihood_fast.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/cov_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/cov_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/c2st.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/c2st.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/c2st_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/c2st_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/c2st_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/c2st_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/c2st_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/c2st_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/c2st_random.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/c2st_random.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/condition_mask_fn/joint.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "joint" -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/condition_mask_fn/likelihood.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "likelihood" -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/condition_mask_fn/posterior.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "posterior" -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/condition_mask_fn/random.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "random" 3 | alpha: 1. 4 | beta: 4. -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/condition_mask_fn/structured_random.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/condition_mask_fn/structured_random.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/cov_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/cov_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/cov_likelihood_fast.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/cov_likelihood_fast.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/cov_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/cov_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/mmd.yaml: -------------------------------------------------------------------------------- 1 | mmd: -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/nll_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/nll_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/nll_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/nll_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/nll_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/metric/nll_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/metric/none.yaml: -------------------------------------------------------------------------------- 1 | 2 | none: 3 | -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_cov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_cov.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_cov_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_cov_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_cov_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_cov_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_likelihood.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_likelihood.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/nll_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/nll_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/eval/none.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/eval/none.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_additional.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_additional.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_additional_nle.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_additional_nle.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_additional_npe.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_additional_npe.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_all_cond.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_all_cond.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_all_cond_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_all_cond_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_all_cond_joint_eval.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_all_cond_joint_eval.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_base.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_base.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_hh.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_hh.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_lv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_lv.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_lv_eval1.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_lv_eval1.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_lv_eval2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_lv_eval2.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_lv_eval3.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_lv_eval3.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_score_base.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_score_base.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_sir.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_sir.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_sir_new.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_sir_new.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_time_steps.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_time_steps.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/bm_time_steps_eval.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/bm_time_steps_eval.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/experiment/example_all_cond.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/experiment/example_all_cond.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/launcher/local.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/launcher/local.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/launcher/slurm.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/launcher/slurm.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/classifier_nn.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/classifier_nn.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/likelihood_nn.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/likelihood_nn.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/posterior_nn.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/posterior_nn.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_mlp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_mlp.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_transformer.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_transformer.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_transformer_large.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_transformer_large.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_transformer_large_token.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_transformer_large_token.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_transformer_small.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_transformer_small.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/model/score_transformer_unconditional.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/model/score_transformer_unconditional.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/nle.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/nle.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/npe.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/npe.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/nre.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/nre.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/nspe.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/nspe.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/backward_ode.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/backward_ode.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/backward_sde.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/backward_sde.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/generalized_guidance.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/generalized_guidance.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/none.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/repaint_sde.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/repaint_sde.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/slice_multi_chain_sbi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/slice_multi_chain_sbi.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/posterior/slice_sbi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/posterior/slice_sbi.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer_directed.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer_directed.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer_joint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer_joint.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer_joint_undirected.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer_joint_undirected.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer_posterior.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer_posterior.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/score_transformer_undirected.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/score_transformer_undirected.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/sde/vesde.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/sde/vesde.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/sde/vpsde.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/sde/vpsde.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/condition_mask_fn/joint.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "joint" -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/condition_mask_fn/likelihood.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "likelihood" -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/condition_mask_fn/posterior.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "posterior" -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/condition_mask_fn/random.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: "random" 3 | alpha: 1. 4 | beta: 4. -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/condition_mask_fn/structured_random.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/condition_mask_fn/structured_random.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/edge_mask_fn/faithfull.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/edge_mask_fn/faithfull.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/edge_mask_fn/min_faithfull.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/edge_mask_fn/min_faithfull.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/edge_mask_fn/none.yaml: -------------------------------------------------------------------------------- 1 | 2 | name: none -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/edge_mask_fn/undirected.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: undirected -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/train_sbi.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/train_sbi.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/train_score_mlp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/train_score_mlp.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/method/train/train_score_transformer.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/method/train/train_score_transformer.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/cpu.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/cpu.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/cpu_long.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/cpu_long.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/cpu_short.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/cpu_short.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/gpu.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/gpu.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/gpu_long.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/gpu_long.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/none.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/scoresbibm/config/partition/v100.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/partition/v100.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/grid.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/grid.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/none.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/none.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/nsga2_mo.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/nsga2_mo.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/random.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/random.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/tpe.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/tpe.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/sweeper/tpe_mo.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/sweeper/tpe_mo.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/task/bernoulli_glm.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: bernoulli_glm 4 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/bernoulli_glm_raw.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: bernoulli_glm_raw 4 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/gaussian_linear.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: gaussian_linear 4 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/gaussian_mixture.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: gaussian_mixture 4 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/hh.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: hh 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/lotka_volterra.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: lotka_volterra 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/marcov_chain_all_cond.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: marcov_chain_all_cond 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/sir.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: sir 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/slcp.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | name: slcp 4 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/slcp_all_cond.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: slcp_all_cond 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/tree_all_cond.yaml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | name: tree_all_cond 5 | num_simulations: 10000 -------------------------------------------------------------------------------- /src/scoresbibm/config/task/two_moons.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/task/two_moons.yaml -------------------------------------------------------------------------------- /src/scoresbibm/config/task/two_moons_all_cond.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/config/task/two_moons_all_cond.yaml -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/evaluation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/evaluation/__init__.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/evaluation/eval_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/evaluation/eval_metrics.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/evaluation/eval_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/evaluation/eval_task.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/guidance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/guidance.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/method_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/method_base.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/models.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/neural_nets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/neural_nets.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/score_sbi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/score_sbi.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/score_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/score_transformer.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/methods/sde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/methods/sde.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | from .hydra_script import main -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/scripts/hydra_script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/scripts/hydra_script.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/__init__.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/all_conditional_tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/all_conditional_tasks.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/base_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/base_task.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/hhtask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/hhtask.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/sbibm_tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/sbibm_tasks.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/tasks/unstructured_tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/tasks/unstructured_tasks.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/__init__.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/condition_masks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/condition_masks.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/data_utils.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/edge_masks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/edge_masks.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/plot.py -------------------------------------------------------------------------------- /src/scoresbibm/scoresbibm/utils/pyloric.mplstyle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/scoresbibm/utils/pyloric.mplstyle -------------------------------------------------------------------------------- /src/scoresbibm/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mackelab/simformer/HEAD/src/scoresbibm/setup.py --------------------------------------------------------------------------------