{
  "schema_version": "pbisc.diffusion_trajectory_annotated_real_reference.v2",
  "status": "completed",
  "title": "PBISC-Diffusion ctx2048 E12 EMA",
  "checkpoint_label": "PBISC-Diffusion ctx2048 E12 EMA",
  "model_genes": 6000,
  "projection_genes": 2980,
  "tracked_cells": 4096,
  "reference_cells": 4362,
  "observed_frames": 51,
  "denoiser_calls_per_tracked_batch": 50,
  "seed": 42,
  "reference": "Observed real PBMCs from the same conditioning donor; GSE135779. These are not generated cells or independent held-out validation.",
  "reference_units": "Observed integer UMI counts; no donor identifier is published.",
  "reference_role": "Only observed reference cells fit every mean, standard deviation, PCA component and UMAP. Tracked generated cells use transform only.",
  "raw_reference_encoding": {
    "max_log_value": 8.0,
    "value_scale": 1.0,
    "center_values": true,
    "support_scale": 1.0,
    "formula": "unit=clip(log1p(observed UMI)/max_log_value,0,1); value=unit/value_scale, then 2*value-1 when centered; support=+support_scale for positive UMI and -support_scale otherwise"
  },
  "raw_projection": "PCA2 fitted once on canonically encoded observed value/support states over common measured genes. Generated noisy states are selected and projected without clipping, rescaling or library normalization.",
  "clean_projection": "Common-gene expression -> expm1(log1p) -> panel sum normalization to 10000 -> log1p -> observed-reference mean/std -> observed-reference PCA30 -> fixed UMAP transform for every generated frame including endpoint.",
  "pca_components": 30,
  "umap": {
    "n_neighbors": 15,
    "min_dist": 0.25,
    "metric": "euclidean",
    "random_state": 42,
    "transform_seed": 42,
    "n_jobs": 1
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  "raw_pca_explained_variance_ratio": [
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  "annotation": {
    "method": "Frozen AIFI scANVI annotation of final generated profiles only",
    "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_2980_v1]",
    "model_sha256": "1e648fba5849b0d0f589eef50b1607d5e3b059aa05e94a0d718e8dfcad477a1b",
    "versions": {
      "scvi-tools": "1.4.1",
      "torch": "2.14.0+cu130",
      "anndata": "0.12.19"
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    "gene_space": {
      "join_key": "ensembl_id",
      "model_genes": 2977,
      "query_genes": 2980,
      "model_genes_missing_from_query_zero_padded": 0,
      "query_genes_outside_model_dropped": 3,
      "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
    },
    "readout": {
      "rule": "One seeded Poisson draw from expm1(endpoint log1p), on the common panel before prediction",
      "seed": 20260916,
      "library_scale": 1.0,
      "raw_observed_counts": false
    },
    "code_to_label": [
      "T cell",
      "B cell",
      "Monocyte",
      "NK cell",
      "DC",
      "Other"
    ],
    "colors": [
      "#0072B2",
      "#D55E00",
      "#009E73",
      "#CC79A7",
      "#E69F00",
      "#56B4E9"
    ],
    "confidence_threshold": 0.0,
    "confidence_semantics": "L2 probability mass summed for the assigned AIFI L1 label. Other combines labels outside PBMC5, without summing all Other probabilities. final_l2_confidence records the L2 maximum separately.",
    "other_semantics": "AIFI annotations outside the specified PBMC5 classes map to Other. Threshold 0 does not reject low-confidence assignments.",
    "temporal_semantics": "Final predicted labels are propagated retrospectively to the same tracked cell IDs; early noisy states are not reclassified.",
    "counts": {
      "T cell": 1578,
      "B cell": 1008,
      "Monocyte": 1234,
      "NK cell": 170,
      "DC": 85,
      "Other": 21
    },
    "confidence_quantiles": {
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      "0.5": 0.9999966025352478,
      "0.9": 0.9999999403953552,
      "1": 1.0
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    "source_schema": "pbisc.trajectory.endpoint_annotation.v1"
  },
  "state_semantics": "Pre-update actual x_t is paired with that call's clean prediction; final x_0 repeats the previous clean prediction. No extra denoiser call at t=0.",
  "axis_limits": "Full min/max across all frames and observed reference points with 6.5% padding, fixed throughout.",
  "repeat_transform_max_abs_difference": 0.0,
  "raw_repeat_transform_max_abs_difference": 0.0,
  "duplicate_prediction_max_abs_difference": 0.0,
  "capture_parity": {
    "status": "passed",
    "cells": 8,
    "steps": 50,
    "device": "cuda:0",
    "returned_tensors_bit_identical": {
      "values": true,
      "dense_values": true,
      "active_mask": true,
      "active_logits": true,
      "final_state": true
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    "rng_unchanged": true,
    "last_decoded_prediction_matches_endpoint": true,
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    "checked_at_utc": "2026-09-17T10:32:13.475853+00:00"
  },
  "provenance": {
    "source_checkpoint_sha256": "f634f0ef06d06cd547e7c53cef58942520f3d998b8d99eba4798ca53fb09f315",
    "checkpoint_sha256": "f093657b435e7ed572370286a39946cdb3ffa7f2b6d2349120ef732795454a1f",
    "condition_sha256": "fb4b0a791ba6e97fec36ebd0f7033d536b7b981eab5ed47b009227bbe891c561",
    "seed": 20260917,
    "weights": "ema",
    "eta": 0.0,
    "capture_manifest_sha256": "f3607992afe390fe9f043323ac305f41df19fa5e36472818ad3c4704633a88e8",
    "renderer_sha256": "ca0ef9baac9468af745c36d8b855ad7f038dff05add89d09b87535a8d59af47c",
    "base_renderer_sha256": "7da598b40d72e3cf7d7004b5ec42f37928dc13b9c517e468d44f0f83c7021930",
    "real_counts_sha256": "208d699a204213dd56e0fb4f40dbf740c331b7cd4ab4998c92cc3280b8de72a9",
    "real_gene_ids_sha256": "c874339c97a97e46eaaf56b2b62dea0311e60dec0af5ab40deb6ff96d7f65508",
    "model_columns_sha256": "2c938250300acea1a4e44e0b7a89ce049c1e31595bdad22d0f384b5604f0a8d8",
    "final_labels_sha256": "954f353e00d436adafefdbcc85d133bed8c0f1eaf3c78aac8b2989ab96d8d0a8",
    "final_confidence_sha256": "7b283b492b3bf100be3faea6c76e7f420bfcaa4f2a0ee2a32823322c33ae2d79",
    "annotation_manifest_sha256": "6b5b2b3275576a63cc29f6307208b3fac29f8ebe1cbd174f4f8cc7201267992c",
    "real_reference_manifest_sha256": "1e95d0d49ec2b254ab5f2a38ac2156c6880044ae0ab071ac8e943f16cec5350a",
    "rendering_code_sha256": "ca0ef9baac9468af745c36d8b855ad7f038dff05add89d09b87535a8d59af47c"
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  "interpretation": [
    "Gray dots are observed real cells from the conditioning donor; they are not independent validation.",
    "Colored cells are generated; PBMC5+Other names are transferred final predictions, not experimentally observed cell identities.",
    "Time is computational denoising, not biological time or differentiation.",
    "Early predictions may lie outside the real reference distribution; UMAP placement does not validate identity or function.",
    "The first clean-expression panel is already a prediction, not Gaussian noise.",
    "Distances use high-dimensional state or expression PCA; UMAP distances are not biological effect sizes."
  ],
  "metric_definitions": {
    "raw_endpoint_rmse": "Mean per-cell RMSE over common measured value/support coordinates to its own endpoint.",
    "expression_endpoint_rmse": "Mean per-cell RMSE in common-panel normalized log1p expression to its own endpoint.",
    "reference_pca_distance_median": "Median nearest-observed-cell Euclidean distance in frozen expression PCA.",
    "support_fraction": "Mean hard support over common measured genes and tracked cells."
  },
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