Remove paper files, output artifacts, pytest cache

.pytest_cache/.gitignore

@@ -1,2 +0,0 @@
-# Created by pytest automatically.
-*

.pytest_cache/CACHEDIR.TAG

@@ -1,4 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55
-# This file is a cache directory tag created by pytest.
-# For information about cache directory tags, see:
-#	https://bford.info/cachedir/spec.html

.pytest_cache/README.md

@@ -1,8 +0,0 @@
-# pytest cache directory #
-
-This directory contains data from the pytest's cache plugin,
-which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
-
-**Do not** commit this to version control.
-
-See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

.pytest_cache/v/cache/lastfailed

@@ -1,3 +0,0 @@
-{
-  "tests/test_beta_groupby.py::test_groupby_consensus_is_median": true
-}

.pytest_cache/v/cache/nodeids

@@ -1,110 +0,0 @@
-[
-  "tests/test_benchmark.py::test_are_enrichment",
-  "tests/test_benchmark.py::test_correlate_no_overlap",
-  "tests/test_benchmark.py::test_correlate_with_halflives",
-  "tests/test_benchmark.py::test_cross_dataset_consistency",
-  "tests/test_benchmark.py::test_enrichment_barplot",
-  "tests/test_benchmark.py::test_halflife_scatter",
-  "tests/test_benchmark.py::test_nmd_enrichment",
-  "tests/test_benchmark.py::test_subsampling_robustness",
-  "tests/test_beta.py::test_estimate_beta",
-  "tests/test_beta.py::test_estimate_beta_quantile",
-  "tests/test_beta_groupby.py::test_groupby_consensus_is_clipped_median",
-  "tests/test_beta_groupby.py::test_groupby_consensus_is_median",
-  "tests/test_beta_groupby.py::test_groupby_missing_column_raises",
-  "tests/test_beta_groupby.py::test_groupby_produces_varm",
-  "tests/test_beta_groupby.py::test_groupby_single_group_matches_global",
-  "tests/test_datasets.py::test_dentate_gyrus_download",
-  "tests/test_datasets.py::test_herzog2017_halflives",
-  "tests/test_datasets.py::test_pancreas_download",
-  "tests/test_datasets.py::test_schofield2018_halflives",
-  "tests/test_deep_data.py::TestGetLibrarySizes::test_correct_sums",
-  "tests/test_deep_data.py::TestGetLibrarySizes::test_missing_layer_raises",
-  "tests/test_deep_data.py::TestGetLibrarySizes::test_positive",
-  "tests/test_deep_data.py::TestGetLibrarySizes::test_shapes",
-  "tests/test_deep_data.py::TestSetupDataloaders::test_batch_contents",
-  "tests/test_deep_data.py::TestSetupDataloaders::test_no_overlap",
-  "tests/test_deep_data.py::TestSetupDataloaders::test_reproducible",
-  "tests/test_deep_data.py::TestSetupDataloaders::test_returns_four",
-  "tests/test_deep_data.py::TestSetupDataloaders::test_stratified_split",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_batch_consistency",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_gradient_flows",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_higher_theta_less_variance",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_non_positive",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_output_shape",
-  "tests/test_deep_distributions.py::TestLogNBPositive::test_peak_at_mean",
-  "tests/test_deep_guide.py::TestExtractLatent::test_deterministic",
-  "tests/test_deep_guide.py::TestExtractLatent::test_no_nans",
-  "tests/test_deep_guide.py::TestExtractLatent::test_shapes",
-  "tests/test_deep_guide.py::TestPosteriorGamma::test_more_samples_lower_variance_of_mean",
-  "tests/test_deep_guide.py::TestPosteriorGamma::test_no_nans",
-  "tests/test_deep_guide.py::TestPosteriorGamma::test_positive_values",
-  "tests/test_deep_guide.py::TestPosteriorGamma::test_shapes",
-  "tests/test_deep_model.py::TestDeepPTR::test_backward",
-  "tests/test_deep_model.py::TestDeepPTR::test_forward_loss",
-  "tests/test_deep_model.py::TestDeepPTR::test_get_latent",
-  "tests/test_deep_model.py::TestDeepPTR::test_kl_weight_zero",
-  "tests/test_deep_model.py::TestDeepPTR::test_reparameterize_stochastic",
-  "tests/test_deep_model.py::TestEncoder::test_different_inputs_different_outputs",
-  "tests/test_deep_model.py::TestEncoder::test_output_shapes",
-  "tests/test_deep_model.py::TestKineticDecoder::test_beta_is_not_cell_specific",
-  "tests/test_deep_model.py::TestKineticDecoder::test_mu_scales_with_library_size",
-  "tests/test_deep_model.py::TestKineticDecoder::test_output_shapes",
-  "tests/test_deep_model.py::TestKineticDecoder::test_positive_outputs",
-  "tests/test_deep_synthetic.py::TestCICoverage::test_perfect_coverage",
-  "tests/test_deep_synthetic.py::TestCICoverage::test_returns_fraction",
-  "tests/test_deep_synthetic.py::TestCICoverage::test_zero_variance_coverage",
-  "tests/test_deep_synthetic.py::TestGammaRecovery::test_global_mode",
-  "tests/test_deep_synthetic.py::TestGammaRecovery::test_perfect_recovery",
-  "tests/test_deep_synthetic.py::TestGammaRecovery::test_random_is_low",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_cell_types",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_non_negative_counts",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_reproducible",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_shapes",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_sparsity",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_truth_keys",
-  "tests/test_deep_synthetic.py::TestGenerateKineticData::test_truth_shapes",
-  "tests/test_deep_synthetic.py::TestLatentRecovery::test_perfect_recovery",
-  "tests/test_deep_synthetic.py::TestLatentRecovery::test_random_is_lower",
-  "tests/test_deep_trainer.py::TestTrainer::test_early_stopping",
-  "tests/test_deep_trainer.py::TestTrainer::test_fit_runs",
-  "tests/test_deep_trainer.py::TestTrainer::test_history_fields",
-  "tests/test_deep_trainer.py::TestTrainer::test_kl_warmup",
-  "tests/test_deep_trainer.py::TestTrainer::test_loss_decreases",
-  "tests/test_gamma.py::test_estimate_gamma",
-  "tests/test_gamma.py::test_gamma_clipping",
-  "tests/test_gamma.py::test_gamma_requires_beta",
-  "tests/test_gamma_dynamic.py::test_dynamic_mode_logs_params",
-  "tests/test_gamma_dynamic.py::test_dynamic_mode_produces_gamma",
-  "tests/test_gamma_dynamic.py::test_dynamic_requires_velocity_layer",
-  "tests/test_gamma_dynamic.py::test_steady_state_mode_default",
-  "tests/test_gamma_dynamic.py::test_unknown_mode_raises",
-  "tests/test_integration.py::test_full_pipeline",
-  "tests/test_integration.py::test_network_inference",
-  "tests/test_network_priors.py::test_list_known_rbps",
-  "tests/test_network_priors.py::test_load_motif_priors_valid",
-  "tests/test_network_priors.py::test_load_motif_priors_validates_columns",
-  "tests/test_network_priors.py::test_network_prior_logs_has_prior",
-  "tests/test_network_priors.py::test_network_with_priors",
-  "tests/test_network_priors.py::test_network_without_priors_unchanged",
-  "tests/test_plotting.py::test_gamma_heatmap",
-  "tests/test_plotting.py::test_gamma_violin",
-  "tests/test_plotting.py::test_phase_portrait",
-  "tests/test_plotting.py::test_pt_comparison",
-  "tests/test_plotting.py::test_pt_umap",
-  "tests/test_plotting.py::test_pt_velocity_embedding",
-  "tests/test_plotting.py::test_pt_velocity_stream",
-  "tests/test_plotting.py::test_tf_ptf_scatter",
-  "tests/test_preprocessing.py::test_filter_cells",
-  "tests/test_preprocessing.py::test_filter_genes",
-  "tests/test_preprocessing.py::test_neighbors",
-  "tests/test_preprocessing.py::test_normalize_layers",
-  "tests/test_preprocessing.py::test_smooth_fixed_bandwidth",
-  "tests/test_preprocessing.py::test_smooth_layers",
-  "tests/test_pt_states.py::test_pt_states",
-  "tests/test_pt_states.py::test_rank_pt_genes",
-  "tests/test_readwrite.py::test_read_h5ad_no_warning_with_layers",
-  "tests/test_readwrite.py::test_read_h5ad_warns_missing_layers",
-  "tests/test_readwrite.py::test_validate_layers_warns_partial",
-  "tests/test_variance.py::test_variance_decomposition"
-]

output/deep_benchmarks/17_go_enrichment/results/go_enrichment.json

@@ -1,509 +0,0 @@
-{
-  "pancreas": {
-    "pt_genes": [
-      "Adgrb3",
-      "Pard3b",
-      "Tmtc2",
-      "Rfx6",
-      "Trim17",
-      "Ptprn2",
-      "Dip2c",
-      "Fhit",
-      "Ube2e2",
-      "Kcnma1",
-      "Farp1",
-      "Rims2",
-      "Igf2bp2",
-      "Stxbp5l",
-      "Phldb2",
-      "Fbxl17",
-      "Park2",
-      "Dnajc1",
-      "Pbx3",
-      "Nr6a1",
-      "Kcnh7",
-      "9030622O22Rik",
-      "Zmynd8",
-      "Mbd5",
-      "Macrod2",
-      "Hnf1aos1",
-      "Sdk1",
-      "Pan3",
-      "Chchd3",
-      "Tmcc1",
-      "Cacna1c",
-      "Snd1",
-      "Ccser1",
-      "Ttll3",
-      "Tmc4",
-      "Egln2",
-      "Gm21974",
-      "Ins2",
-      "Kcnq1",
-      "Fam155a",
-      "Wwox",
-      "Tcf12",
-      "Rora",
-      "Mid1"
-    ],
-    "organism": "mmusculus",
-    "go_terms": [
-      {
-        "source": "TF",
-        "native": "TF:M04157_1",
-        "name": "Factor: Tfap2a; motif: TGCCCYNRGGGCA; match class: 1",
-        "p_value": 3.466458557901524e-05,
-        "intersection_size": 25
-      },
-      {
-        "source": "TF",
-        "native": "TF:M03893",
-        "name": "Factor: WT1; motif: GNGGGGGCGGGG",
-        "p_value": 0.00035020125807490933,
-        "intersection_size": 28
-      },
-      {
-        "source": "GO:BP",
-        "native": "GO:0009306",
-        "name": "protein secretion",
-        "p_value": 0.0005506951793064151,
-        "intersection_size": 8
-      },
-      {
-        "source": "GO:BP",
-        "native": "GO:0035592",
-        "name": "establishment of protein localization to extracellular region",
-        "p_value": 0.0005817536873480544,
-        "intersection_size": 8
-      },
-      {
-        "source": "TF",
-        "native": "TF:M02933",
-        "name": "Factor: ZF5; motif: GYCGCGCARNGCNN",
-        "p_value": 0.000604116486020235,
-        "intersection_size": 33
-      },
-      {
-        "source": "TF",
-        "native": "TF:M05494_1",
-        "name": "Factor: Egr-2; motif: GCGTGGGCGG; match class: 1",
-        "p_value": 0.0006381914250372045,
-        "intersection_size": 18
-      },
-      {
-        "source": "GO:BP",
-        "native": "GO:0071692",
-        "name": "protein localization to extracellular region",
-        "p_value": 0.0006484043265494617,
-        "intersection_size": 8
-      },
-      {
-        "source": "TF",
-        "native": "TF:M03567",
-        "name": "Factor: Sp2; motif: NYSGCCCCGCCCCCY",
-        "p_value": 0.0008218740122645273,
-        "intersection_size": 27
-      },
-      {
-        "source": "TF",
-        "native": "TF:M00982",
-        "name": "Factor: KROX; motif: CCCGCCCCCRCCCC",
-        "p_value": 0.0008861792328755127,
-        "intersection_size": 26
-      },
-      {
-        "source": "KEGG",
-        "native": "KEGG:04911",
-        "name": "Insulin secretion",
-        "p_value": 0.0009743376454725036,
-        "intersection_size": 4
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10211",
-        "name": "Factor: E2F-4; motif: NGGGGGCGGGRMNN",
-        "p_value": 0.001079688451739799,
-        "intersection_size": 28
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10213",
-        "name": "Factor: Egr-1; motif: NNGCGKGGGCGGGG",
-        "p_value": 0.0012241500134068221,
-        "intersection_size": 22
-      },
-      {
-        "source": "TF",
-        "native": "TF:M07395_1",
-        "name": "Factor: Sp1; motif: NGGGGCGGGGN; match class: 1",
-        "p_value": 0.002317847212801588,
-        "intersection_size": 22
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10211_1",
-        "name": "Factor: E2F-4; motif: NGGGGGCGGGRMNN; match class: 1",
-        "p_value": 0.00235674928913849,
-        "intersection_size": 16
-      },
-      {
-        "source": "TF",
-        "native": "TF:M05494",
-        "name": "Factor: Egr-2; motif: GCGTGGGCGG",
-        "p_value": 0.002435404573586561,
-        "intersection_size": 28
-      },
-      {
-        "source": "TF",
-        "native": "TF:M02933_1",
-        "name": "Factor: ZF5; motif: GYCGCGCARNGCNN; match class: 1",
-        "p_value": 0.0026093353609088744,
-        "intersection_size": 25
-      },
-      {
-        "source": "TF",
-        "native": "TF:M02744",
-        "name": "Factor: Egr1; motif: NCCGCCCCCGCANN",
-        "p_value": 0.0027636846535903366,
-        "intersection_size": 19
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10278_1",
-        "name": "Factor: KLF3; motif: NNNNNNGGGCGGGGCNNGN; match class: 1",
-        "p_value": 0.003393074052401255,
-        "intersection_size": 18
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10375_1",
-        "name": "Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG; match class: 1",
-        "p_value": 0.003822518456117497,
-        "intersection_size": 28
-      },
-      {
-        "source": "TF",
-        "native": "TF:M10212",
-        "name": "Factor: E2F-7; motif: GRGGCGGGAANNN",
-        "p_value": 0.004049920835981174,
-        "intersection_size": 29
-      }
-    ],
-    "n_significant": 65,
-    "module_go": [
-      {
-        "module": 0,
-        "n_genes": 459,
-        "top_terms": [
-          "chemical homeostasis",
-          "Spinocerebellar ataxia",
-          "voltage-gated monoatomic cation channel activity"
-        ],
-        "top_rbps": [
-          [
-            "MATR3",
-            151
-          ],
-          [
-            "ELAVL1",
-            133
-          ],
-          [
-            "RBFOX2",
-            121
-          ]
-        ]
-      },
-      {
-        "module": 1,
-        "n_genes": 6,
-        "top_terms": [],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            5
-          ],
-          [
-            "MATR3",
-            4
-          ],
-          [
-            "HNRNPC",
-            3
-          ]
-        ]
-      },
-      {
-        "module": 2,
-        "n_genes": 6,
-        "top_terms": [
-          "sterol sensor activity",
-          "lipid sensor activity"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            2
-          ],
-          [
-            "HNRNPC",
-            2
-          ],
-          [
-            "MATR3",
-            2
-          ]
-        ]
-      },
-      {
-        "module": 3,
-        "n_genes": 8,
-        "top_terms": [
-          "Factor: AP-2beta; motif: GCNNNGGSCNGVGGGN"
-        ],
-        "top_rbps": [
-          [
-            "MATR3",
-            3
-          ],
-          [
-            "ELAVL1",
-            1
-          ],
-          [
-            "FUS",
-            1
-          ]
-        ]
-      },
-      {
-        "module": 7,
-        "n_genes": 6,
-        "top_terms": [
-          "Factor: Sp2; motif: NYSGCCCCGCCCCCY; match class: 1",
-          "Factor: AP2; motif: GCCYGSGGSN; match class: 1",
-          "Factor: SP1; motif: GGGGYGGGGNS; match class: 1"
-        ],
-        "top_rbps": [
-          [
-            "HNRNPC",
-            5
-          ],
-          [
-            "RBFOX2",
-            4
-          ],
-          [
-            "ELAVL1",
-            3
-          ]
-        ]
-      },
-      {
-        "module": 8,
-        "n_genes": 5,
-        "top_terms": [
-          "DNA Damage Reversal",
-          "Reversal of alkylation damage by DNA dioxygenases"
-        ],
-        "top_rbps": [
-          [
-            "MATR3",
-            3
-          ],
-          [
-            "RBFOX2",
-            3
-          ],
-          [
-            "ELAVL1",
-            2
-          ]
-        ]
-      }
-    ]
-  },
-  "dentate_gyrus": {
-    "pt_genes": [
-      "Eml6",
-      "Cnot6",
-      "Scfd1",
-      "Nrxn3",
-      "Kcnma1",
-      "Cacnb2",
-      "Taf13",
-      "Rmdn1",
-      "Palm2",
-      "Cdh8",
-      "Tmem108"
-    ],
-    "organism": "mmusculus",
-    "go_terms": [
-      {
-        "source": "GO:MF",
-        "native": "GO:0005246",
-        "name": "calcium channel regulator activity",
-        "p_value": 0.022776740344038288,
-        "intersection_size": 2
-      },
-      {
-        "source": "GO:MF",
-        "native": "GO:0005515",
-        "name": "protein binding",
-        "p_value": 0.030353353140200337,
-        "intersection_size": 10
-      }
-    ],
-    "n_significant": 2,
-    "module_go": [
-      {
-        "module": 0,
-        "n_genes": 1266,
-        "top_terms": [],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            380
-          ],
-          [
-            "MATR3",
-            301
-          ],
-          [
-            "RBFOX2",
-            260
-          ]
-        ]
-      },
-      {
-        "module": 1,
-        "n_genes": 19,
-        "top_terms": [
-          "Factor: E2F; motif: NNTTTCGCGCN",
-          "exonuclease activity",
-          "squalene synthase [NAD(P)H] activity"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            7
-          ],
-          [
-            "MATR3",
-            7
-          ],
-          [
-            "HNRNPC",
-            3
-          ]
-        ]
-      },
-      {
-        "module": 3,
-        "n_genes": 9,
-        "top_terms": [
-          "Factor: Egr-2; motif: GCGTGGGCGG",
-          "Factor: USF; motif: GYCACGTGNC",
-          "malate synthase activity"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            5
-          ],
-          [
-            "MATR3",
-            3
-          ],
-          [
-            "HNRNPC",
-            2
-          ]
-        ]
-      },
-      {
-        "module": 5,
-        "n_genes": 9,
-        "top_terms": [
-          "Factor: HIF-1alpha; motif: GNACGTGM",
-          "dihydrolipoyllysine-residue acetyltransferase activity",
-          "Grb7-Elavl1  complex"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            4
-          ],
-          [
-            "MATR3",
-            4
-          ],
-          [
-            "FUS",
-            2
-          ]
-        ]
-      },
-      {
-        "module": 6,
-        "n_genes": 8,
-        "top_terms": [
-          "Factor: ER81; motif: RCCGGAWRYN",
-          "methyl/ethyl malonyl-CoA decarboxylase activity"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            3
-          ],
-          [
-            "MATR3",
-            2
-          ]
-        ]
-      },
-      {
-        "module": 8,
-        "n_genes": 5,
-        "top_terms": [
-          "mitogen-activated protein kinase kinase kinase binding",
-          "Oligodactyly",
-          "Ccd1-Dvl2 complex"
-        ],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            2
-          ],
-          [
-            "MATR3",
-            2
-          ],
-          [
-            "FUS",
-            1
-          ]
-        ]
-      },
-      {
-        "module": 9,
-        "n_genes": 6,
-        "top_terms": [],
-        "top_rbps": [
-          [
-            "ELAVL1",
-            3
-          ],
-          [
-            "MATR3",
-            2
-          ],
-          [
-            "RBFOX2",
-            2
-          ]
-        ]
-      }
-    ]
-  }
-}

output/deep_benchmarks/18_halflife_ceiling/results/halflife_ceiling.json

@@ -1,19 +0,0 @@
-{
-  "inter_study_r": 0.7666700848697275,
-  "inter_study_r_log": 0.7802797873918921,
-  "inter_study_n": 10608,
-  "inter_study_ci": [
-    0.7574056787467361,
-    0.7748092949600333
-  ],
-  "method_ceiling_pct": {
-    "scPTR analytical (pancreas, human)": 52.447592248016925,
-    "scPTR analytical (DG, human)": 49.721517445769834,
-    "scVelo SS (pancreas, human)": 48.65195699704132,
-    "scVelo SS (DG, human)": 47.93456889118682,
-    "velVI (pancreas, human)": 36.29983815623753,
-    "velVI (DG, human)": 45.938925614900675,
-    "DeepPTR (pancreas, human)": 36.0911434345344,
-    "DeepPTR (DG, human)": 46.65631372075517
-  }
-}

output/deep_benchmarks/19_scvelo_dyn_investigation/results/scvelo_dyn_investigation.json

@@ -1,3 +0,0 @@
-{
-  "note": "Investigation complete, see stdout"
-}

output/deep_benchmarks/20_uncertainty_advantage/results/uncertainty_advantage.json

@@ -1,76 +0,0 @@
-{
-  "pancreas": {
-    "analytical_300": {
-      "r": -0.22231279755152644,
-      "n": 219
-    },
-    "deepptr_all": {
-      "r": -0.2767452667406712,
-      "n": 236
-    },
-    "deepptr_filtered": [
-      {
-        "percentile": 75,
-        "r": -0.2935350818803388,
-        "n": 180,
-        "cv_cutoff": 0.11798103153705597
-      },
-      {
-        "percentile": 50,
-        "r": -0.2784230794623337,
-        "n": 120,
-        "cv_cutoff": 0.09954803436994553
-      },
-      {
-        "percentile": 25,
-        "r": -0.3779708509647762,
-        "n": 53,
-        "cv_cutoff": 0.08271166682243347
-      },
-      {
-        "percentile": 10,
-        "r": -0.2781954887218045,
-        "n": 20,
-        "cv_cutoff": 0.05375545844435692
-      }
-    ],
-    "improvement": 0.15565805341324973
-  },
-  "dentate_gyrus": {
-    "analytical_300": {
-      "r": -0.3593371092867718,
-      "n": 199
-    },
-    "deepptr_all": {
-      "r": -0.35768791768630437,
-      "n": 211
-    },
-    "deepptr_filtered": [
-      {
-        "percentile": 75,
-        "r": -0.4037010444550779,
-        "n": 159,
-        "cv_cutoff": 0.13886773586273193
-      },
-      {
-        "percentile": 50,
-        "r": -0.3379248062565652,
-        "n": 100,
-        "cv_cutoff": 0.11725422739982605
-      },
-      {
-        "percentile": 25,
-        "r": -0.10556391748122433,
-        "n": 49,
-        "cv_cutoff": 0.0847647488117218
-      },
-      {
-        "percentile": 10,
-        "r": 0.004511278195488721,
-        "n": 20,
-        "cv_cutoff": 0.029071299359202385
-      }
-    ],
-    "improvement": 0.04436393516830606
-  }
-}

output/deep_benchmarks/21_identifiability/results/identifiability.json

@@ -1,52 +0,0 @@
-{
-  "pancreas": {
-    "real": {
-      "sil_T": 0.20693553984165192,
-      "sil_PT": -0.006579563952982426,
-      "ari": 0.1888022197849624,
-      "n_pt_genes": 45
-    },
-    "permuted": [
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-        "sil_PT": -0.06523298472166061,
-        "ari": 0.0015657809737397933
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-      {
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-        "sil_PT": -0.24032162129878998,
-        "ari": -0.00065230249262882
-      },
-      {
-        "sil_T": -0.09248553216457367,
-        "sil_PT": -0.5077192187309265,
-        "ari": -0.0021321385037561614
-      }
-    ]
-  },
-  "dentate_gyrus": {
-    "real": {
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-      "sil_PT": 0.04487254470586777,
-      "ari": 0.2758917875838645,
-      "n_pt_genes": 11
-    },
-    "permuted": [
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-        "ari": -0.0008575691119994391
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-      {
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-        "sil_PT": -0.2607710659503937,
-        "ari": -0.005626463263878278
-      },
-      {
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-        "sil_PT": -0.16378729045391083,
-        "ari": 0.002526632428011187
-      }
-    ]
-  }
-}

output/deep_benchmarks/22_partial_correlation/results/partial_correlation.json

@@ -1,46 +0,0 @@
-{
-  "pancreas": {
-    "scptr": {
-      "raw_r": -0.4020872107350974,
-      "raw_p": 3.872107573583121e-167,
-      "partial_r": -0.1536742103004309,
-      "partial_p": 3.529388954295092e-24,
-      "partial_ci_lo": -0.18279121514175428,
-      "partial_ci_hi": -0.12209239328943841,
-      "n": 4308,
-      "expression_confound": 0.2484130004346665
-    },
-    "scvelo_ss": {
-      "raw_r": -0.37302647517581816,
-      "raw_p": 1.2211299844635986e-51,
-      "partial_r": -0.1906281174559328,
-      "partial_p": 5.713074784106551e-14,
-      "partial_ci_lo": -0.238967747105761,
-      "partial_ci_hi": -0.1444090472293224,
-      "n": 1528,
-      "expression_confound": 0.18239835771988536
-    }
-  },
-  "dentate_gyrus": {
-    "scptr": {
-      "raw_r": -0.3812073018847205,
-      "raw_p": 2.9304430684031824e-40,
-      "partial_r": -0.15338225997017077,
-      "partial_p": 2.3185149712748635e-07,
-      "partial_ci_lo": -0.20713324950124962,
-      "partial_ci_hi": -0.0995441394072433,
-      "n": 1126,
-      "expression_confound": 0.22782504191454975
-    },
-    "scvelo_ss": {
-      "raw_r": -0.3674575813971968,
-      "raw_p": 2.5778985987233377e-51,
-      "partial_r": -0.17998235709789673,
-      "partial_p": 6.973047679364984e-13,
-      "partial_ci_lo": -0.22801156039845,
-      "partial_ci_hi": -0.13371732874391323,
-      "n": 1568,
-      "expression_confound": 0.18747522429930008
-    }
-  }
-}

output/deep_benchmarks/23_beta_vae/results/beta_vae.json

@@ -1,98 +0,0 @@
-{
-  "sweep": [
-    {
-      "beta_kl": 1.0,
-      "coverage_train": 0.24504666666666666,
-      "coverage_test": 0.24098,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
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-      "coverage_train": 0.45587333333333335,
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-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 3.0,
-      "coverage_train": 0.61084,
-      "coverage_test": 0.60724,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 5.0,
-      "coverage_train": 0.7918666666666667,
-      "coverage_test": 0.78946,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 8.0,
-      "coverage_train": 0.90706,
-      "coverage_test": 0.9000733333333333,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 10.0,
-      "coverage_train": 0.9420733333333333,
-      "coverage_test": 0.9333533333333334,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 15.0,
-      "coverage_train": 0.9796666666666667,
-      "coverage_test": 0.9719266666666667,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    },
-    {
-      "beta_kl": 20.0,
-      "coverage_train": 0.9917666666666667,
-      "coverage_test": 0.98624,
-      "gamma_r_train": 0.853620590942485,
-      "gamma_r_test": 0.869201669867409
-    }
-  ],
-  "best_beta": 10.0,
-  "calibration_curve": [
-    {
-      "level": 0.5,
-      "raw": 0.08406,
-      "calibrated": 0.6598533333333333
-    },
-    {
-      "level": 0.6,
-      "raw": 0.1043,
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-    {
-      "level": 0.7,
-      "raw": 0.12798,
-      "calibrated": 0.8054066666666667
-    },
-    {
-      "level": 0.8,
-      "raw": 0.15860666666666667,
-      "calibrated": 0.8605
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-    {
-      "level": 0.9,
-      "raw": 0.2025,
-      "calibrated": 0.9081866666666667
-    },
-    {
-      "level": 0.95,
-      "raw": 0.24098,
-      "calibrated": 0.9333533333333334
-    },
-    {
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-      "raw": 0.31317333333333336,
-      "calibrated": 0.96226
-    }
-  ]
-}

output/deep_benchmarks/24_fullgenome_gpu/results/fullgenome_gpu.json

@@ -1,112 +0,0 @@
-{
-  "pancreas": [
-    {
-      "n_genes": 300,
-      "label": "300 genes",
-      "device": "cpu",
-      "time_s": 126.28486108779907,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.19762101977653473,
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-      "hl_human_r": -0.2767452667406712,
-      "hl_human_n": 236
-    },
-    {
-      "n_genes": 500,
-      "label": "500 genes",
-      "device": "cpu",
-      "time_s": 195.14217829704285,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.13388556817704766,
-      "hl_mouse_n": 425,
-      "hl_human_r": -0.23868475929802593,
-      "hl_human_n": 405
-    },
-    {
-      "n_genes": 1000,
-      "label": "1000 genes",
-      "device": "cpu",
-      "time_s": 250.388201713562,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.1749767413418925,
-      "hl_mouse_n": 855,
-      "hl_human_r": -0.2701509996732806,
-      "hl_human_n": 828
-    },
-    {
-      "n_genes": 2000,
-      "label": "2000 genes",
-      "device": "cpu",
-      "time_s": 311.9621741771698,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.2015269295525831,
-      "hl_mouse_n": 1732,
-      "hl_human_r": -0.29089533198701906,
-      "hl_human_n": 1653
-    },
-    {
-      "n_genes": 11906,
-      "label": "Analytical (all)",
-      "device": "cpu",
-      "hl_mouse_r": -0.34966929477006137,
-      "hl_human_r": -0.4020872107350974,
-      "hl_mouse_n": 4611,
-      "hl_human_n": 4308
-    }
-  ],
-  "dentate_gyrus": [
-    {
-      "n_genes": 300,
-      "label": "300 genes",
-      "device": "cpu",
-      "time_s": 177.58326506614685,
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-      "hl_mouse_n": 216,
-      "hl_human_r": -0.35768791768630437,
-      "hl_human_n": 211
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-    {
-      "n_genes": 500,
-      "label": "500 genes",
-      "device": "cpu",
-      "time_s": 101.45515847206116,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.32213690425879954,
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-      "hl_human_n": 361
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-    {
-      "n_genes": 1000,
-      "label": "1000 genes",
-      "device": "cpu",
-      "time_s": 215.91462779045105,
-      "n_epochs": 100,
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-      "hl_human_n": 752
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-    {
-      "n_genes": 2000,
-      "label": "2000 genes",
-      "device": "cpu",
-      "time_s": 244.55135011672974,
-      "n_epochs": 100,
-      "hl_mouse_r": -0.3052852382518734,
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-      "hl_human_r": -0.3678329895976058,
-      "hl_human_n": 1542
-    },
-    {
-      "n_genes": 5325,
-      "label": "Analytical (all)",
-      "device": "cpu",
-      "hl_mouse_r": -0.3179587682344816,
-      "hl_human_r": -0.3812073018847205,
-      "hl_mouse_n": 1217,
-      "hl_human_n": 1126
-    }
-  ]
-}

output/deep_benchmarks/25_scvelo_dyn_sweep/results/scvelo_dyn_sweep.json

@@ -1,118 +0,0 @@
-{
-  "pancreas": {
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-        "n_top_genes": 500,
-        "n_valid_gamma": 421,
-        "hl_mouse_r": 0.0015232299632728275,
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-        "hl_human_r": -0.07127067836395753,
-        "hl_human_n": 268,
-        "mean_fit_likelihood": 0.28437144651282054,
-        "n_low_likelihood": 24
-      },
-      {
-        "n_top_genes": 1000,
-        "n_valid_gamma": 824,
-        "hl_mouse_r": 0.08201653274084658,
-        "hl_mouse_n": 646,
-        "hl_human_r": 0.03550756870945792,
-        "hl_human_n": 575,
-        "mean_fit_likelihood": 0.277095819711648,
-        "n_low_likelihood": 32
-      },
-      {
-        "n_top_genes": 1500,
-        "n_valid_gamma": 1095,
-        "hl_mouse_r": 0.09158090791457907,
-        "hl_mouse_n": 869,
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-        "hl_human_n": 783,
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-        "n_low_likelihood": 37
-      },
-      {
-        "n_top_genes": 2000,
-        "n_valid_gamma": 1298,
-        "hl_mouse_r": 0.08206325739571528,
-        "hl_mouse_n": 1048,
-        "hl_human_r": 0.07312700187874449,
-        "hl_human_n": 955,
-        "mean_fit_likelihood": 0.2679284916372894,
-        "n_low_likelihood": 41
-      },
-      {
-        "n_top_genes": 3000,
-        "n_valid_gamma": 1591,
-        "hl_mouse_r": 0.06290554803201429,
-        "hl_mouse_n": 1322,
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-        "hl_human_n": 1212,
-        "mean_fit_likelihood": 0.2629648387133424,
-        "n_low_likelihood": 44
-      }
-    ],
-    "steady_state": {
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-      "hl_human_r": -0.37302647517581816
-    }
-  },
-  "dentate_gyrus": {
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-        "n_valid_gamma": 243,
-        "hl_mouse_r": 0.20143188003913634,
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-        "n_valid_gamma": 489,
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-        "n_low_likelihood": 208
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-        "n_valid_gamma": 975,
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-        "mean_fit_likelihood": 0.1639305921458248,
-        "n_low_likelihood": 253
-      },
-      {
-        "n_top_genes": 3000,
-        "n_valid_gamma": 1373,
-        "hl_mouse_r": -0.04109758385476612,
-        "hl_mouse_n": 1120,
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-        "n_low_likelihood": 325
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-    "steady_state": {
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-    }
-  }
-}

output/deep_benchmarks/26_large_atlas/results/large_atlas.json

@@ -1,44 +0,0 @@
-{
-  "n_total_cells": 33130,
-  "n_total_genes": 12295,
-  "analytical_time": 155.5868625640869,
-  "analytical_r": -0.39535873582128667,
-  "deep_scaling": [
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-      "n_cells": 5000,
-      "n_genes": 300,
-      "device": "cpu",
-      "time_s": 143.60735058784485,
-      "hl_r": -0.3266187303287622,
-      "hl_n": 240,
-      "n_epochs": 100
-    },
-    {
-      "n_cells": 10000,
-      "n_genes": 300,
-      "device": "cpu",
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-      "hl_r": -0.3294859694739123,
-      "hl_n": 240,
-      "n_epochs": 100
-    },
-    {
-      "n_cells": 20000,
-      "n_genes": 300,
-      "device": "cpu",
-      "time_s": 822.7187304496765,
-      "hl_r": -0.3303235186374605,
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-    },
-    {
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-      "n_genes": 300,
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-      "time_s": 1070.3793358802795,
-      "hl_r": -0.31406792619020274,
-      "hl_n": 239,
-      "n_epochs": 100
-    }
-  ]
-}

output/deep_benchmarks/27_perturbation_validation/results/perturbation_validation.json

@@ -1,240 +0,0 @@
-{
-  "pancreas": {
-    "rbp_enrichment": [
-      {
-        "rbp": "MATR3",
-        "n_targets_in_data": 1656,
-        "n_pt_targets": 17,
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-        "p_adjusted": 0.011082036273963083
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-      {
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-        "p_adjusted": 0.026325116726982133
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-      {
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-        "p_adjusted": 0.08161886263925526
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-      {
-        "rbp": "HNRNPC",
-        "n_targets_in_data": 1386,
-        "n_pt_targets": 9,
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-      },
-      {
-        "rbp": "MBNL2",
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-      {
-        "rbp": "RBFOX2",
-        "n_targets_in_data": 2075,
-        "n_pt_targets": 12,
-        "odds_ratio": 1.7812045564711585,
-        "p_value": 0.06911573320035953,
-        "p_adjusted": 0.0888630855433194
-      },
-      {
-        "rbp": "TRA2B",
-        "n_targets_in_data": 636,
-        "n_pt_targets": 3,
-        "odds_ratio": 1.298000231187146,
-        "p_value": 0.4199408479134497,
-        "p_adjusted": 0.43666530224668393
-      },
-      {
-        "rbp": "HNRNPA1",
-        "n_targets_in_data": 154,
-        "n_pt_targets": 1,
-        "odds_ratio": 1.7797537619699042,
-        "p_value": 0.43666530224668393,
-        "p_adjusted": 0.43666530224668393
-      }
-    ],
-    "gamma_comparisons": [
-      {
-        "rbp": "MATR3",
-        "n_targets": 1149,
-        "median_gamma_targets": 1.5993330478668213,
-        "median_gamma_background": 0.5209805965423584,
-        "fold_change": 3.0698513984680176,
-        "mannwhitney_p": 1.8820073302083007e-38
-      },
-      {
-        "rbp": "FUS",
-        "n_targets": 492,
-        "median_gamma_targets": 0.7054176330566406,
-        "median_gamma_background": 0.6999531984329224,
-        "fold_change": 1.0078068971633911,
-        "mannwhitney_p": 0.36606400288814334
-      },
-      {
-        "rbp": "HNRNPU",
-        "n_targets": 132,
-        "median_gamma_targets": 1.4246070384979248,
-        "median_gamma_background": 0.6980903148651123,
-        "fold_change": 2.040720224380493,
-        "mannwhitney_p": 0.0012413221423628004
-      },
-      {
-        "rbp": "ELAVL1",
-        "n_targets": 1559,
-        "median_gamma_targets": 0.7672077417373657,
-        "median_gamma_background": 0.6624136567115784,
-        "fold_change": 1.1582003831863403,
-        "mannwhitney_p": 0.020664531992697802
-      },
-      {
-        "rbp": "HNRNPC",
-        "n_targets": 1003,
-        "median_gamma_targets": 1.0293357372283936,
-        "median_gamma_background": 0.6238839030265808,
-        "fold_change": 1.649883508682251,
-        "mannwhitney_p": 3.504914176404013e-07
-      }
-    ],
-    "n_pt_genes": 44
-  },
-  "dentate_gyrus": {
-    "rbp_enrichment": [
-      {
-        "rbp": "HNRNPA1",
-        "n_targets_in_data": 74,
-        "n_pt_targets": 1,
-        "odds_ratio": 7.17945205479452,
-        "p_value": 0.1427980120016106,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "MATR3",
-        "n_targets_in_data": 928,
-        "n_pt_targets": 3,
-        "odds_ratio": 1.7793243243243244,
-        "p_value": 0.29767143659701994,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "HNRNPC",
-        "n_targets_in_data": 750,
-        "n_pt_targets": 2,
-        "odds_ratio": 1.35650623885918,
-        "p_value": 0.47237207296965444,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "TRA2B",
-        "n_targets_in_data": 392,
-        "n_pt_targets": 1,
-        "odds_ratio": 1.259079283887468,
-        "p_value": 0.5691266871558499,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "ELAVL1",
-        "n_targets_in_data": 1267,
-        "n_pt_targets": 2,
-        "odds_ratio": 0.7112867808519983,
-        "p_value": 0.7770620444588854,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "RBFOX2",
-        "n_targets_in_data": 949,
-        "n_pt_targets": 1,
-        "odds_ratio": 0.46054852320675105,
-        "p_value": 0.8848243929650565,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "FUS",
-        "n_targets_in_data": 343,
-        "n_pt_targets": 0,
-        "odds_ratio": 0.0,
-        "p_value": 1.0,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "HNRNPU",
-        "n_targets_in_data": 106,
-        "n_pt_targets": 0,
-        "odds_ratio": 0.0,
-        "p_value": 1.0,
-        "p_adjusted": 1.0
-      },
-      {
-        "rbp": "MBNL2",
-        "n_targets_in_data": 196,
-        "n_pt_targets": 0,
-        "odds_ratio": 0.0,
-        "p_value": 1.0,
-        "p_adjusted": 1.0
-      }
-    ],
-    "gamma_comparisons": [
-      {
-        "rbp": "HNRNPA1",
-        "n_targets": 23,
-        "median_gamma_targets": 0.8581850528717041,
-        "median_gamma_background": 0.6610870361328125,
-        "fold_change": 1.2981423139572144,
-        "mannwhitney_p": 0.3325841180912675
-      },
-      {
-        "rbp": "MATR3",
-        "n_targets": 327,
-        "median_gamma_targets": 0.7761924266815186,
-        "median_gamma_background": 0.6090543866157532,
-        "fold_change": 1.2744221687316895,
-        "mannwhitney_p": 0.025610764991262094
-      },
-      {
-        "rbp": "HNRNPC",
-        "n_targets": 258,
-        "median_gamma_targets": 0.6743285059928894,
-        "median_gamma_background": 0.6598281264305115,
-        "fold_change": 1.0219759941101074,
-        "mannwhitney_p": 0.32161339672935296
-      },
-      {
-        "rbp": "TRA2B",
-        "n_targets": 147,
-        "median_gamma_targets": 0.4067135453224182,
-        "median_gamma_background": 0.7446471452713013,
-        "fold_change": 0.5461829304695129,
-        "mannwhitney_p": 0.9999437281596838
-      },
-      {
-        "rbp": "ELAVL1",
-        "n_targets": 424,
-        "median_gamma_targets": 0.5818213820457458,
-        "median_gamma_background": 0.7141801118850708,
-        "fold_change": 0.8146703839302063,
-        "mannwhitney_p": 0.8700806334555964
-      }
-    ],
-    "n_pt_genes": 11
-  }
-}

output/deep_benchmarks/28_gamma_semantics/results/gamma_semantics.json

@@ -1,58 +0,0 @@
-{
-  "pancreas": {
-    "scptr_vs_scvelo_ss": {
-      "r": 0.9614689055885701,
-      "n": 1145
-    },
-    "scvelo_ss_vs_dyn": {
-      "r": -0.36667693072256663,
-      "n": 1298
-    },
-    "halflife": {
-      "scPTR gamma": {
-        "r": -0.4020872107350974,
-        "n": 4308
-      },
-      "scVelo SS velocity_gamma": {
-        "r": -0.37302647517581816,
-        "n": 1528
-      },
-      "scVelo dyn fit_gamma (raw)": {
-        "r": 0.07312700187874449,
-        "n": 955
-      },
-      "scVelo dyn fit_gamma/fit_beta": {
-        "r": -0.3457372034025884,
-        "n": 955
-      }
-    }
-  },
-  "dentate_gyrus": {
-    "scptr_vs_scvelo_ss": {
-      "r": 0.8775771932216537,
-      "n": 812
-    },
-    "scvelo_ss_vs_dyn": {
-      "r": -0.09013762620050701,
-      "n": 975
-    },
-    "halflife": {
-      "scPTR gamma": {
-        "r": -0.3812073018847205,
-        "n": 1126
-      },
-      "scVelo SS velocity_gamma": {
-        "r": -0.3674575813971968,
-        "n": 1568
-      },
-      "scVelo dyn fit_gamma (raw)": {
-        "r": -0.05706868509199329,
-        "n": 719
-      },
-      "scVelo dyn fit_gamma/fit_beta": {
-        "r": -0.34677476243451283,
-        "n": 719
-      }
-    }
-  }
-}

output/deep_benchmarks/29_pt_states_comparison/results/pt_states_comparison.json

@@ -1,53 +0,0 @@
-{
-  "pancreas": {
-    "scptr_n_clusters": 15,
-    "scvelo_n_clusters": 16,
-    "scptr_invisible": [
-      "1",
-      "4",
-      "6",
-      "12"
-    ],
-    "scvelo_invisible": [
-      "0",
-      "1",
-      "2",
-      "4",
-      "5",
-      "8",
-      "11"
-    ],
-    "ari_scptr_vs_scvelo": 0.23362857400039413,
-    "nmi_scptr_vs_scvelo": 0.4465821668717804,
-    "ari_scptr_vs_expr": 0.2812235448672833,
-    "ari_scvelo_vs_expr": 0.2032717487099801
-  },
-  "dentate_gyrus": {
-    "scptr_n_clusters": 18,
-    "scvelo_n_clusters": 19,
-    "scptr_invisible": [
-      "0",
-      "2",
-      "4",
-      "5",
-      "7",
-      "9",
-      "12",
-      "13"
-    ],
-    "scvelo_invisible": [
-      "0",
-      "3",
-      "6",
-      "9",
-      "10",
-      "11",
-      "12",
-      "13"
-    ],
-    "ari_scptr_vs_scvelo": 0.07712124784892622,
-    "nmi_scptr_vs_scvelo": 0.2300609069761501,
-    "ari_scptr_vs_expr": 0.16889465914979085,
-    "ari_scvelo_vs_expr": 0.12285852551694108
-  }
-}

output/deep_benchmarks/30_crossval/results/crossval.json

@@ -1,102 +0,0 @@
-{
-  "pancreas": {
-    "r_full": -0.4020872107350974,
-    "r_train_mean": -0.4025614306526538,
-    "r_test_mean": -0.3999093124584256,
-    "r_test_std": 0.001018524545889871,
-    "r_agreement": 0.9992720121770591,
-    "generalization_gap": 0.0026521181942282257,
-    "folds": [
-      {
-        "fold": 0,
-        "r_train": -0.4032881687390775,
-        "r_test": -0.3993354385634667,
-        "r_agreement": 0.9992153146807581,
-        "n_train": 2957,
-        "n_test": 739
-      },
-      {
-        "fold": 1,
-        "r_train": -0.4025750465845809,
-        "r_test": -0.3984741463559988,
-        "r_agreement": 0.9992684691552222,
-        "n_train": 2957,
-        "n_test": 739
-      },
-      {
-        "fold": 2,
-        "r_train": -0.4026846600177091,
-        "r_test": -0.3998480690173671,
-        "r_agreement": 0.9993107703855446,
-        "n_train": 2957,
-        "n_test": 739
-      },
-      {
-        "fold": 3,
-        "r_train": -0.40202232482040523,
-        "r_test": -0.40151504192164944,
-        "r_agreement": 0.9992356742812513,
-        "n_train": 2957,
-        "n_test": 739
-      },
-      {
-        "fold": 4,
-        "r_train": -0.40223695310149615,
-        "r_test": -0.40037386643364575,
-        "r_agreement": 0.9993298323825188,
-        "n_train": 2957,
-        "n_test": 739
-      }
-    ]
-  },
-  "dentate_gyrus": {
-    "r_full": -0.3812073018847205,
-    "r_train_mean": -0.3809802087704274,
-    "r_test_mean": -0.37730992195900837,
-    "r_test_std": 0.008896236902592808,
-    "r_agreement": 0.9975205259374503,
-    "generalization_gap": 0.00367028681141901,
-    "folds": [
-      {
-        "fold": 0,
-        "r_train": -0.37824783969263287,
-        "r_test": -0.37465932477354197,
-        "r_agreement": 0.9970905050622035,
-        "n_train": 2344,
-        "n_test": 586
-      },
-      {
-        "fold": 1,
-        "r_train": -0.3792536490666531,
-        "r_test": -0.3878162384574487,
-        "r_agreement": 0.9979650343606248,
-        "n_train": 2344,
-        "n_test": 586
-      },
-      {
-        "fold": 2,
-        "r_train": -0.38048737006004496,
-        "r_test": -0.3826819304902708,
-        "r_agreement": 0.9977655530016082,
-        "n_train": 2344,
-        "n_test": 586
-      },
-      {
-        "fold": 3,
-        "r_train": -0.38535863483396265,
-        "r_test": -0.36169711544040367,
-        "r_agreement": 0.9966872165833951,
-        "n_train": 2344,
-        "n_test": 586
-      },
-      {
-        "fold": 4,
-        "r_train": -0.3815535501988434,
-        "r_test": -0.3796950006333766,
-        "r_agreement": 0.9980943206794197,
-        "n_train": 2344,
-        "n_test": 586
-      }
-    ]
-  }
-}

output/deep_benchmarks/31_method_difference/results/method_difference.json

@@ -1,49 +0,0 @@
-{
-  "differences": [
-    {
-      "aspect": "Gene filtering",
-      "scvelo": "HVG selection (2000 genes)",
-      "scptr": "Unspliced count filter (11906 genes)",
-      "impact": "scPTR uses 9906 more genes"
-    },
-    {
-      "aspect": "Smoothing",
-      "scvelo": "kNN moments (connectivities-weighted)",
-      "scptr": "kNN Gaussian-kernel smoothing",
-      "impact": "Different kernel weights, but similar result"
-    },
-    {
-      "aspect": "Gamma formula",
-      "scvelo": "velocity_gamma = regression slope of Mu vs Ms (per-gene)",
-      "scptr": "gamma_ig = beta_g * Mu_ig / Ms_ig (per-cell, per-gene)",
-      "impact": "scPTR: per-cell values enable clustering. scVelo: single value per gene."
-    },
-    {
-      "aspect": "Beta (splicing rate)",
-      "scvelo": "Implicitly 1 (absorbed into gamma)",
-      "scptr": "Explicit quantile regression (0.95 quantile of u/s slope), then multiplied into gamma",
-      "impact": "scPTR gamma = beta * Mu/Ms, scVelo gamma = Mu/Ms slope. Rank correlation r=0.96."
-    },
-    {
-      "aspect": "Outlier control",
-      "scvelo": "None for velocity_gamma",
-      "scptr": "Two-stage: per-gene 99th pctl + global 10x cap",
-      "impact": "Prevents extreme gamma values from dominating downstream analysis"
-    },
-    {
-      "aspect": "Output granularity",
-      "scvelo": "Per-gene gamma (single value in adata.var)",
-      "scptr": "Per-cell, per-gene gamma matrix (adata.layers['gamma'])",
-      "impact": "Enables: PT state clustering, PT velocity, cell-type-specific analysis"
-    },
-    {
-      "aspect": "Downstream analysis",
-      "scvelo": "Velocity vectors, velocity graph, latent time",
-      "scptr": "PT states, PT velocity, variance decomposition, RBP networks, DeepPTR",
-      "impact": "Different analytical framework: degradation-centric vs velocity-centric"
-    }
-  ],
-  "beta_cv": 1.492958426475525,
-  "gamma_correlation": 0.96,
-  "clipping_fraction": 0.554664564885252
-}

output/deep_benchmarks/32_sparsity_control/results/sparsity_control.json

@@ -1,102 +0,0 @@
-{
-  "pancreas": [
-    {
-      "label": "A. Full gamma",
-      "n_clusters": 15,
-      "n_invisible": 4,
-      "ari_vs_expr": 0.30167626726893315,
-      "nmi_vs_expr": 0.5379586275584342,
-      "silhouette": 0.07287579029798508
-    },
-    {
-      "label": "B. Dense genes (5080)",
-      "n_clusters": 10,
-      "n_invisible": 2,
-      "ari_vs_expr": 0.3865853615965537,
-      "nmi_vs_expr": 0.577930851691227,
-      "silhouette": 0.040946368128061295
-    },
-    {
-      "label": "C. Very dense genes (2708)",
-      "n_clusters": 8,
-      "n_invisible": 5,
-      "ari_vs_expr": 0.4110133968397583,
-      "nmi_vs_expr": 0.4319633334033957,
-      "silhouette": -0.005909333936870098
-    },
-    {
-      "label": "D. Binarized (0/1)",
-      "n_clusters": 27,
-      "n_invisible": 2,
-      "ari_vs_expr": 0.295599500154883,
-      "nmi_vs_expr": 0.6234740407466665,
-      "silhouette": 0.24341168999671936
-    },
-    {
-      "label": "E. Zero-permuted",
-      "n_clusters": 9,
-      "n_invisible": 9,
-      "ari_vs_expr": -0.001505489648143163,
-      "nmi_vs_expr": 0.003872916118906932,
-      "silhouette": -0.02439497411251068
-    },
-    {
-      "label": "F. Log gamma",
-      "n_clusters": 24,
-      "n_invisible": 1,
-      "ari_vs_expr": 0.3386094074131817,
-      "nmi_vs_expr": 0.6471045086700452,
-      "silhouette": 0.24840642511844635
-    }
-  ],
-  "dentate_gyrus": [
-    {
-      "label": "A. Full gamma",
-      "n_clusters": 18,
-      "n_invisible": 8,
-      "ari_vs_expr": 0.15138261601931394,
-      "nmi_vs_expr": 0.38872016562396877,
-      "silhouette": -0.016102824360132217
-    },
-    {
-      "label": "B. Dense genes (1416)",
-      "n_clusters": 16,
-      "n_invisible": 5,
-      "ari_vs_expr": 0.153993308831925,
-      "nmi_vs_expr": 0.398965341581588,
-      "silhouette": -0.036132000386714935
-    },
-    {
-      "label": "C. Very dense genes (410)",
-      "n_clusters": 18,
-      "n_invisible": 9,
-      "ari_vs_expr": 0.13728754106809862,
-      "nmi_vs_expr": 0.3555261084765987,
-      "silhouette": -0.06208645924925804
-    },
-    {
-      "label": "D. Binarized (0/1)",
-      "n_clusters": 24,
-      "n_invisible": 3,
-      "ari_vs_expr": 0.19209279255313694,
-      "nmi_vs_expr": 0.5307952912744213,
-      "silhouette": 0.010215776041150093
-    },
-    {
-      "label": "E. Zero-permuted",
-      "n_clusters": 13,
-      "n_invisible": 13,
-      "ari_vs_expr": -5.528328000990069e-05,
-      "nmi_vs_expr": 0.013679112102514431,
-      "silhouette": -0.052636608481407166
-    },
-    {
-      "label": "F. Log gamma",
-      "n_clusters": 21,
-      "n_invisible": 3,
-      "ari_vs_expr": 0.2416888573635724,
-      "nmi_vs_expr": 0.5669973786130235,
-      "silhouette": 0.08507860451936722
-    }
-  ]
-}

output/deep_benchmarks/33_percell_advantage/results/percell_advantage.json

@@ -1,146 +0,0 @@
-{
-  "pancreas": {
-    "r_global": -0.4020872107350974,
-    "ct_halflife": [
-      {
-        "cell_type": "Alpha",
-        "n_cells": 481,
-        "r": -0.40280853512977915,
-        "n_genes": 4561
-      },
-      {
-        "cell_type": "Beta",
-        "n_cells": 591,
-        "r": -0.39947748625767454,
-        "n_genes": 4697
-      },
-      {
-        "cell_type": "Delta",
-        "n_cells": 70,
-        "r": -0.3891139485465312,
-        "n_genes": 4578
-      },
-      {
-        "cell_type": "Ductal",
-        "n_cells": 916,
-        "r": -0.40035253751218247,
-        "n_genes": 4446
-      },
-      {
-        "cell_type": "Epsilon",
-        "n_cells": 142,
-        "r": -0.4074290859499848,
-        "n_genes": 4641
-      },
-      {
-        "cell_type": "Ngn3 high EP",
-        "n_cells": 642,
-        "r": -0.38567677362906416,
-        "n_genes": 3846
-      },
-      {
-        "cell_type": "Ngn3 low EP",
-        "n_cells": 262,
-        "r": -0.3925242796464273,
-        "n_genes": 4245
-      },
-      {
-        "cell_type": "Pre-endocrine",
-        "n_cells": 592,
-        "r": -0.4011497591510283,
-        "n_genes": 4203
-      }
-    ],
-    "ct_range": 0.02175231232092062,
-    "n_transition": 289,
-    "n_pure": 2079,
-    "frac_within_gene_var": 0.7156800031661987
-  },
-  "dentate_gyrus": {
-    "r_global": -0.3812073018847205,
-    "ct_halflife": [
-      {
-        "cell_type": "Astrocytes",
-        "n_cells": 120,
-        "r": -0.44038042300897623,
-        "n_genes": 615
-      },
-      {
-        "cell_type": "Cajal Retzius",
-        "n_cells": 34,
-        "r": -0.4123640954361777,
-        "n_genes": 699
-      },
-      {
-        "cell_type": "Cck-Tox",
-        "n_cells": 27,
-        "r": -0.36859355592063603,
-        "n_genes": 1248
-      },
-      {
-        "cell_type": "Endothelial",
-        "n_cells": 87,
-        "r": -0.39310134422108817,
-        "n_genes": 847
-      },
-      {
-        "cell_type": "GABA",
-        "n_cells": 61,
-        "r": -0.38905809943427455,
-        "n_genes": 1951
-      },
-      {
-        "cell_type": "Granule immature",
-        "n_cells": 785,
-        "r": -0.3717157477095277,
-        "n_genes": 1502
-      },
-      {
-        "cell_type": "Granule mature",
-        "n_cells": 1070,
-        "r": -0.36901341949611155,
-        "n_genes": 1171
-      },
-      {
-        "cell_type": "Microglia",
-        "n_cells": 81,
-        "r": -0.4371866960934686,
-        "n_genes": 455
-      },
-      {
-        "cell_type": "Mossy",
-        "n_cells": 75,
-        "r": -0.3617548069145115,
-        "n_genes": 2384
-      },
-      {
-        "cell_type": "Neuroblast",
-        "n_cells": 417,
-        "r": -0.40888234084715314,
-        "n_genes": 970
-      },
-      {
-        "cell_type": "OL",
-        "n_cells": 50,
-        "r": -0.3532647181848459,
-        "n_genes": 845
-      },
-      {
-        "cell_type": "OPC",
-        "n_cells": 53,
-        "r": -0.3517639400116957,
-        "n_genes": 794
-      },
-      {
-        "cell_type": "Radial Glia-like",
-        "n_cells": 51,
-        "r": -0.3889722826079631,
-        "n_genes": 794
-      }
-    ],
-    "ct_range": 0.08861648299728053,
-    "n_transition": 461,
-    "n_pure": 1066,
-    "frac_within_gene_var": 0.6811126470565796
-  }
-}

output/deep_benchmarks/34_beta_contribution/results/beta_contribution.json

@@ -1,26 +0,0 @@
-{
-  "pancreas": {
-    "naive_mouse": -0.3337539045489983,
-    "naive_human": -0.3819000674302124,
-    "scptr_mouse": -0.34966929477006137,
-    "scptr_human": -0.4020872107350974,
-    "beta_improvement_mouse": 0.015915390221063086,
-    "beta_improvement_human": 0.020187143304885025,
-    "sil_naive": -0.04342705592959113,
-    "sil_scptr": 0.07388103753328323,
-    "beta_cv": 1.492958426475525,
-    "naive_scptr_agreement": 0.981253807062886
-  },
-  "dentate_gyrus": {
-    "naive_mouse": -0.27818291707155846,
-    "naive_human": -0.34373895555772266,
-    "scptr_mouse": -0.3179587682344816,
-    "scptr_human": -0.3812073018847205,
-    "beta_improvement_mouse": 0.03977585116292315,
-    "beta_improvement_human": 0.03746834632699786,
-    "sil_naive": -0.03820189249760528,
-    "sil_scptr": -0.018672795966267586,
-    "beta_cv": 1.1358402967453003,
-    "naive_scptr_agreement": 0.9730293885468464
-  }
-}

output/deep_benchmarks/35_corrected_comparison/results/corrected_comparison.json

@@ -1,50 +0,0 @@
-{
-  "pancreas": {
-    "global_halflife": {
-      "scvelo_ss": {
-        "r": -0.37302647517581816,
-        "n": 1528
-      },
-      "scvelo_dyn_raw": {
-        "r": 0.07312700187874449,
-        "n": 955
-      },
-      "scvelo_dyn_corrected": {
-        "r": -0.3457372034025884,
-        "n": 955
-      },
-      "scptr": {
-        "r": -0.4020872107350974,
-        "n": 4308
-      }
-    },
-    "best_celltype": {
-      "cell_type": "Epsilon",
-      "r": -0.4074290859499848
-    }
-  },
-  "dentate_gyrus": {
-    "global_halflife": {
-      "scvelo_ss": {
-        "r": -0.3674575813971968,
-        "n": 1568
-      },
-      "scvelo_dyn_raw": {
-        "r": -0.05706868509199329,
-        "n": 719
-      },
-      "scvelo_dyn_corrected": {
-        "r": -0.34677476243451283,
-        "n": 719
-      },
-      "scptr": {
-        "r": -0.3812073018847205,
-        "n": 1126
-      }
-    },
-    "best_celltype": {
-      "cell_type": "Astrocytes",
-      "r": -0.44038042300897623
-    }
-  }
-}