{ "protocol": { "epochs": 120, "synthetic_seeds": [ 301, 302, 303 ], "real_model_seeds": [ 71, 72, 73 ], "methods": [ "upstream_decipher", "rna_only", "joint", "normalized_dropout", "multivi", "rna_pca", "atac_lsi" ], "settings": "Frozen previous defaults; no new hyperparameter search. Validation ELBO chooses checkpoint only.", "dimensions": "Native Decipher v=2 and z=6. MultiVI native z=6, v denotes training-fitted PCA2. PCA/LSI use first 2 or 6 components.", "geometry": "Original repository mean intercluster-distance Kendall metric; clusters from truth for scoring only, test rows scored.", "ordering": "Training-only 15-NN graph plus MST connectivity edges, rooted at mean immature training anchors; test cells attach to nearest train cell. Signed Spearman, no test-informed reversal.", "branch": "Exploratory 20-centroid MST junction estimate; root failure gets absolute error 1. This is not a validated lineage-inference method.", "trends": "Common train-only 15-neighbor expression smoother versus expected noise-free simulated log-panel10k expression. Separate native v-to-z-to-RNA decoder score where available.", "uncertainty": "Three matched simulations and fits; t intervals across runs. Real data uses three initializations of one technical-group split, not biological replication.", "paper_check": "Pinned lab generator and metric; 3 seeds x 5 sparsity levels. Current upstream architecture, six latent dimensions, held-out scoring and reduced epoch budget. Adapted check, not full Figure 2 reproduction.", "source_sha256": "9e6cfaebe62bc47e278e2a662d389c627b86e644dc68b81a035bccd1cad3f30a" }, "sources": { "scripts\\export_trajectory_website.py": "af3e198faed5bf386c308bf8f3667f35e21198d37198941d1767479512dfc8ed", "scripts\\run_trajectory_benchmark.py": "9e6cfaebe62bc47e278e2a662d389c627b86e644dc68b81a035bccd1cad3f30a", "scripts\\run_followup_benchmark.py": "877b91613f4a257242f23ba6e77b20f99181b7d0d73e7fa90765895916bf066a", "scripts\\run_public_multiome_benchmark.py": "e9a9736e3b615e30f08afbc05e272cfe229d9329e836365313900368108317d1", "scripts\\run_ablation_benchmark.py": "9d284af3d722ea85bbd4c73363a0757adc01392605fece2688ca6f01c32196c6", "decipher\\tools\\multiome.py": "772fa92da521bc22032ac810e224375b09cc23b85edb1cc05eeea86ec8b24f9b", "decipher\\tools\\_decipher\\decipher.py": "056586fda50a31c1252afa66da304bf5e5fecc404a93d606687d4367713593a0", "decipher\\tools\\_multiome\\__init__.py": 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