*.7z filter=lfs diff=lfs merge=lfs -text *.arrow filter=lfs diff=lfs merge=lfs -text *.bin filter=lfs diff=lfs merge=lfs -text *.bz2 filter=lfs diff=lfs merge=lfs -text *.ckpt filter=lfs diff=lfs merge=lfs -text *.ftz filter=lfs diff=lfs merge=lfs -text *.gz filter=lfs diff=lfs merge=lfs -text *.h5 filter=lfs diff=lfs merge=lfs -text *.joblib filter=lfs diff=lfs merge=lfs -text *.lfs.* filter=lfs diff=lfs merge=lfs -text *.mlmodel filter=lfs diff=lfs merge=lfs -text *.model filter=lfs diff=lfs merge=lfs -text *.msgpack filter=lfs diff=lfs merge=lfs -text *.npy filter=lfs diff=lfs merge=lfs -text *.npz filter=lfs diff=lfs merge=lfs -text *.onnx filter=lfs diff=lfs merge=lfs -text *.ot filter=lfs diff=lfs merge=lfs -text *.parquet filter=lfs diff=lfs merge=lfs -text *.pb filter=lfs diff=lfs merge=lfs -text *.pickle filter=lfs diff=lfs merge=lfs -text *.pkl filter=lfs diff=lfs merge=lfs -text *.pt filter=lfs diff=lfs merge=lfs -text *.pth filter=lfs diff=lfs merge=lfs -text *.rar filter=lfs diff=lfs merge=lfs -text *.safetensors filter=lfs diff=lfs merge=lfs -text saved_model/**/* filter=lfs diff=lfs merge=lfs -text *.tar.* filter=lfs diff=lfs merge=lfs -text *.tar filter=lfs diff=lfs merge=lfs -text *.tflite filter=lfs diff=lfs merge=lfs -text *.tgz filter=lfs diff=lfs merge=lfs -text *.wasm filter=lfs diff=lfs merge=lfs -text *.xz filter=lfs diff=lfs merge=lfs -text *.zip filter=lfs diff=lfs merge=lfs -text *.zst filter=lfs diff=lfs merge=lfs -text *tfevents* filter=lfs diff=lfs merge=lfs -text output/gap_analysis/figures/invisible_states/invisible_states_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmark_v2/figures/dentate_gyrus_latent_spaces.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmark_v2/figures/pancreas_latent_spaces.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/dentate_gyrus_cell_resolution.png filter=lfs diff=lfs merge=lfs -text output/mirna_analysis/figures/mirna_analysis_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/precedence/figures/example_genes_pancreas.png filter=lfs diff=lfs merge=lfs -text output/weakness_improvements/figures/depmap_stratified.png filter=lfs diff=lfs merge=lfs -text output/tier1_fixes/figures/ablation_pancreas.png filter=lfs diff=lfs merge=lfs -text output/tier1_fixes/figures/velocity_streamlines_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/scifate_validation/figures/scifate_gamma_vs_ground_truth.png filter=lfs diff=lfs merge=lfs -text output/tier1_fixes/figures/ablation_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/tier1_fixes/figures/velocity_streamlines_pancreas.png filter=lfs diff=lfs merge=lfs -text output/scifate_validation/figures/scifate_per_timepoint.png filter=lfs diff=lfs merge=lfs -text output/mirna_analysis/figures/mirna_analysis_pancreas.png filter=lfs diff=lfs merge=lfs -text output/dentate_gyrus/figures/halflife_scatter.png filter=lfs diff=lfs merge=lfs -text output/dentate_gyrus/figures/pt_velocity_embedding.png filter=lfs diff=lfs merge=lfs -text output/dentate_gyrus/figures/pt_umap.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/09_gamma_coexpression/figures/pancreas_gamma_corr.png filter=lfs diff=lfs merge=lfs -text .pybiomart.sqlite filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/12_method_comparison/figures/dentate_gyrus_method_comparison.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/28_gamma_semantics/figures/pancreas_gamma_semantics.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/23_beta_vae/figures/beta_vae.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/18_halflife_ceiling/figures/halflife_ceiling.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/28_gamma_semantics/figures/dentate_gyrus_gamma_semantics.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/12_method_comparison/figures/pancreas_method_comparison.png filter=lfs diff=lfs merge=lfs -text output/comprehensive_fixes/figures/per_cell_scifate.png filter=lfs diff=lfs merge=lfs -text output/remaining_validation/figures/groupby_beta_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/remaining_validation/figures/groupby_beta_pancreas.png filter=lfs diff=lfs merge=lfs -text output/comprehensive_fixes/figures/utr_network_validation.png filter=lfs diff=lfs merge=lfs -text output/comprehensive_fixes/figures/hub_consistency.png filter=lfs diff=lfs merge=lfs -text output/velocity_comparison/figures/streamlines_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/velocity_comparison/figures/streamlines_pancreas.png filter=lfs diff=lfs merge=lfs -text data/Pancreas/endocrinogenesis_day15.h5ad filter=lfs diff=lfs merge=lfs -text example_paper.pdf filter=lfs diff=lfs merge=lfs -text output/gap_analysis/figures/invisible_states/invisible_states_pancreas.png filter=lfs diff=lfs merge=lfs -text output/cross_dataset/cross_dataset_scatter.png filter=lfs diff=lfs merge=lfs -text output/gap_analysis/figures/velocity_comparison/velocity_comparison_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/gap_analysis/figures/velocity_comparison/velocity_comparison_pancreas.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/pancreas_disentanglement.png filter=lfs diff=lfs merge=lfs -text output/precedence/figures/example_genes_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/pancreas_posterior_testing.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/dentate_gyrus_posterior_testing.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/dentate_gyrus_disentanglement.png filter=lfs diff=lfs merge=lfs -text output/deep_advantages/figures/pancreas_cell_resolution.png filter=lfs diff=lfs merge=lfs -text output/weakness_fixes/figures/destabilizing_bias_fix_pancreas.png filter=lfs diff=lfs merge=lfs -text output/tier2_validation/figures/seq_features_pancreas.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmark/figures/scifate_comparison.png filter=lfs diff=lfs merge=lfs -text output/tier2_validation/figures/seq_features_dentate_gyrus.png filter=lfs diff=lfs merge=lfs -text output/figures/aim1/halflife_scatter.png filter=lfs diff=lfs merge=lfs -text output/tier3/figures/neuroblastoma_corrected_overview.png filter=lfs diff=lfs merge=lfs -text output/tier3/figures/depmap_scatter.png filter=lfs diff=lfs merge=lfs -text output/figures/aim3/pt_velocity_embedding.png filter=lfs diff=lfs merge=lfs -text output/tier2_validation/figures/seq_features_scifate.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/08_temporal_latent/figures/pancreas_temporal.png filter=lfs diff=lfs merge=lfs -text output/tier3/figures/neuroblastoma_overview.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/20_uncertainty_advantage/figures/pancreas_uncertainty_advantage.png filter=lfs diff=lfs merge=lfs -text output/figures/aim2/pt_umap.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/04_scifate_tautology/figures/scifate_tautology.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/07_reconstruction/figures/dentate_gyrus_reconstruction.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/09_gamma_coexpression/figures/dentate_gyrus_gamma_corr.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/20_uncertainty_advantage/figures/dentate_gyrus_uncertainty_advantage.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/11_expression_vs_gamma/figures/dentate_gyrus_expr_vs_gamma.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/08_temporal_latent/figures/dentate_gyrus_temporal.png filter=lfs diff=lfs merge=lfs -text data/DentateGyrus/10X43_1.h5ad filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/07_reconstruction/figures/pancreas_reconstruction.png filter=lfs diff=lfs merge=lfs -text output/deep_benchmarks/11_expression_vs_gamma/figures/pancreas_expr_vs_gamma.png filter=lfs diff=lfs merge=lfs -text