release: publish Stage-1 continuous v3.0.1

Supersedes v2 on main while preserving v2 by immutable tag and history. Stage-1-only; continuous scores; no categorical cell calls or Stage-2–4 outputs.

LICENSE

@@ -1,23 +1,28 @@
 MIT License
 
-Copyright (c) 2025 The upstream authors of "Primary Human CD4+ T Cell Perturb-seq"
-  (Zhu, Dann, Yan, Reyes Retana, Goto, Guitche, Petersen, Ota, Shy, Pritchard, Marson;
-   CZI Virtual Cells Platform) — for the underlying data.
-Copyright (c) 2026 Kirit Singh — for the derived NTC-subset, scVI-embedded object and
-  the spot Stage-1 pipeline.
+Copyright (c) 2026 Kirit Singh
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this
-dataset and associated documentation files (the "Dataset"), to deal in the Dataset
-without restriction, including without limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of the Dataset, and to permit persons
-to whom the Dataset is furnished to do so, subject to the following conditions:
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all copies or
-substantial portions of the Dataset.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+This license applies to spot-authored transformations, metadata, and release
+packaging. The underlying public source dataset retains its upstream license.
+The official CZI Virtual Cells Platform page declares that dataset MIT-licensed
+but does not provide an exact upstream copyright-holder notice; none is inferred
+here. See NOTICE for source attribution.
 
-THE DATASET IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
-INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
-PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
-FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATASET OR THE USE OR OTHER
-DEALINGS IN THE DATASET.

MANIFEST.json

@@ -1,9 +1,233 @@
 {
-  "method_version": "stage1-continuous-v2",
-  "supersedes": "prior HF revision (retains history; see card retractions)",
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-  "outputs": {"stage01_umap_seed.json": {"n_cells": 40000, "content": "continuous transcriptional-program scores + display-only colour key"}},
-  "reproducibility": {"seed": 12345, "pythonhashseed": 0, "canonical_table_sha256": "6e1665d13eab1781407b43d232d089fb5fb6a6b9df5acd83cbbfb8fe3aed2755", "barcode_set_sha256": "1224312e52231f4b2e07c192b39c6f9c69dd6e2d5b8bd64d936c17a9b2435a93"},
-  "disclaimer": "Continuous transcriptional-program scores; exploratory; NOT validated cell-type calls. RNA compatibility does not demonstrate lineage stability, protein expression, cytotoxicity, or suppressive function.",
-  "code": "github.com/Kirit-Singh/spot @ branch stage1-remediation"
+  "schema": "spot.hf_stage1_release_manifest.v1",
+  "release_id": "stage1-continuous-v3.0.1",
+  "release_date": "2026-07-13",
+  "release_tag": "stage1-continuous-v3.0.1",
+  "scope": "Stage 1 only: continuous CD4 transcriptional-program scoring",
+  "source_repository": "https://github.com/Kirit-Singh/spot",
+  "source_repository_commit": "29bd367b6e0ed674868041a4fe85d1f6fafd4cb8",
+  "historical_v2": {
+    "hf_revision": "e5fcf98b56a9302921d402e97fc5a190bd88f9a6",
+    "release_tag": "stage1-continuous-v2",
+    "current_tree_action": "remove root stage01_umap_seed.json; preserve it in history and the v2 tag"
+  },
+  "upstream": {
+    "dataset": "Primary Human CD4+ T Cell Perturb-seq",
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+    "portal_version": "v1.0",
+    "portal_release_date": "2025-12-22",
+    "portal_declared_license": "MIT License",
+    "preprint_doi": "10.64898/2025.12.23.696273"
+  },
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+  "privacy": {
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 }

NOTICE

@@ -1,18 +1,32 @@
-NOTICE — third-party attributions
-
-This dataset is DERIVED from:
-  "Primary Human CD4+ T Cell Perturb-seq" (Marson GWCD4i) — Zhu, Dann, ... Marson (2025),
-  CZI Virtual Cells Platform (billion-cell-project, v1.0.0, 2025-12-22).
-  Upstream license: MIT (https://mit-license.org/), per the dataset's Croissant metadata.
-  Cite: bioRxiv doi:10.64898/2025.12.23.696273.
-
-Upstream MIT permission notice (preserved):
-  Permission is hereby granted, free of charge, to any person obtaining a copy of this
-  data and associated documentation, to deal in it without restriction, including the
-  rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies,
-  subject to: the above copyright notice and this permission notice shall be included in
-  all copies or substantial portions. THE DATA IS PROVIDED "AS IS", WITHOUT WARRANTY.
-
-spot's derived transformations (subsetting, embedding, clustering, continuous program
-scoring) are (c) 2026 Kirit Singh, licensed MIT (see LICENSE). This NOTICE is provided as
-a sensible third-party attribution; MIT does not itself mandate a separate NOTICE file.
+NOTICE — third-party source and attribution
+
+This release is derived from the public dataset:
+
+  Primary Human CD4+ T Cell Perturb-seq
+  CZI Virtual Cells Platform, v1.0, released 22 December 2025
+  https://virtualcellmodels.cziscience.com/dataset/genome-scale-tcell-perturb-seq
+
+Associated publication:
+
+  Zhu, Dann, et al. Genome-scale perturb-seq in primary human CD4+ T cells maps
+  context-specific regulators of T cell programs and human immune traits.
+  bioRxiv 2025.12.23.696273.
+  https://doi.org/10.64898/2025.12.23.696273
+
+Associated analysis code:
+
+  https://github.com/emdann/GWT_perturbseq_analysis_2025
+
+The official CZI dataset page declares the source dataset licensed under the
+MIT License. It does not provide an exact upstream copyright-holder notice on
+the public landing page. This file therefore records the declaration and
+attribution without inventing a holder or claiming to reproduce a notice
+verbatim.
+
+The spot-derived quota-balanced NTC object, continuous program scores, method
+metadata, validation artifacts, and release packaging are copyright (c) 2026
+Kirit Singh and are licensed under the MIT License in LICENSE.
+
+The program registry cites scientific papers as provenance. Those citations do
+not bundle the cited papers or transfer their copyrights or licenses.
+

README.md

@@ -1,103 +1,176 @@
 ---
 license: mit
-pretty_name: spot 01_programs — CD4 NTC embedded object + continuous program scores
-tags: [single-cell, immunology, perturb-seq, CD4-T-cells, scVI, reproducibility, exploratory]
-size_categories: [100K<n<1M]
-source_datasets: [CZI Virtual Cells Platform — Primary Human CD4+ T Cell Perturb-seq (Marson GWCD4i)]
-language: [en]
-annotations_creators: [machine-generated]
+pretty_name: spot Stage 1 — CD4 continuous transcriptional-program scores
+tags:
+  - single-cell
+  - immunology
+  - perturb-seq
+  - CD4-T-cells
+  - transcriptomics
+  - reproducibility
+size_categories:
+  - 100K<n<1M
+source_datasets:
+  - CZI Virtual Cells Platform — Primary Human CD4+ T Cell Perturb-seq
+language:
+  - en
+annotations_creators:
+  - machine-generated
 ---
 
-# spot · 01_programs — CD4 NTC embedded object + continuous transcriptional-program scores
-
-The embedded, clustered non-targeting-control (NTC) CD4⁺ T cells that the spot Stage-1 workbench
-scores, plus the workbench's **continuous transcriptional-program scores**. This is an
-**exploratory program-scoring** substrate, **not** a validated cell-type classifier.
-
-> **RNA program-compatibility does not demonstrate lineage stability, protein expression,
-> cytotoxicity, or suppressive function.**
-
-## ⚠ Superseding revision — retractions (2026-07)
-
-This revision **supersedes** the previous one (the earlier artifact remains in the immutable HF
-history; it is not being pretended away). We **retract** these prior claims, which were found
-false on review:
-
-- ~~"paper-exact" embedding / "reproduces Supplementary Figure 2"~~ → the embedding is
-  **spot-specific and paper-inspired**, not a verbatim reproduction (see below).
-- ~~"CP10k and median normalization give byte-identical calls"~~ → **false**: `log1p(αx)` is not a
-  global shift; a genuine CP10k run changes ~1% of the prior categorical calls. Median
-  normalization is the frozen method; CP10k is a **sensitivity analysis**, not an identity.
-- ~~"byte-reproducible / 100% cell-for-cell"~~ → the prior verifier only compared aggregate
-  counts (a zero-cell overlay passed at "100%"). Reproduction now verifies a **per-barcode**
-  canonical table.
-- ~~calibrated functional-subtype "cell-type calls" / forced Treg cluster / permutation-FDR
-  q-values~~ → **withdrawn**: the outputs are now **continuous program scores only** (no
-  categorical calls, no p/q, no forced labels, no prevalence).
-
-Important validation remains outstanding: leave-one-donor-out, activation-matched calibration,
-external-dataset confirmation, and protein/functional evidence. Stage-1 is an **exploratory
-candidate-program workbench, not a locked or confirmed biological taxonomy**.
-
-## Source & derivation
-
-Derived from the Marson GWCD4i genome-scale CRISPRi Perturb-seq dataset ("Primary Human CD4+ T
-Cell Perturb-seq", CZI Virtual Cells Platform, `billion-cell-project`, v1.0.0, 2025-12-22):
-- Portal: https://virtualcellmodels.cziscience.com/dataset/genome-scale-tcell-perturb-seq
-- Preprint: Zhu, Dann, … Marson, bioRxiv 2025.12.23.696273, doi:10.64898/2025.12.23.696273
-- Authors' analysis code: https://github.com/emdann/GWT_perturbseq_analysis_2025
-
-**Subset:** non-targeting-control cells only, **spot's quota-balanced sample** — 132,000 per
-condition (Rest/Stim8hr/Stim48hr) = **396,000**, across 4 donors. This is *not* the authors' NTC
-population weighting (their Methods sample ~395,030 NTC cells); percentages in the workbench are
-prevalences in an **equal-weighted spot sample**, not in the source population. Genome: GRCh38.
-
-## Embedding recipe (spot-specific, paper-inspired — NOT paper-exact)
-
-scVI **architecture** values match the authors' (n_latent=30, n_layers=2, n_hidden=128,
-dropout=0.2, NB, batch=donor, 5000 seurat_v3 HVGs) → 100-NN UMAP. But this is **not a verbatim
-reproduction**: the executed host script did not confirm several of the authors' training
-settings against their notebook, `scvi.settings.seed=0` is spot's addition (the authors set
-none), and the **Leiden-0.8 clustering is spot's own** (the authors embed but do not cluster the
-NTC cells). Treat it as "paper-inspired, spot-clustered." The scVI latent space is not
-byte-reproducible (no author seed).
-
-## Normalization
-
-`.X` = the authors' default-median `normalize_total()` (per-cell total → median ≈ 9,819) + `log1p`
-on raw counts. **CP10k (`target_sum=1e4`) is a sensitivity analysis, not an identity** — it
-changes ~1% of the prior categorical calls, because `log1p(αx)` is not a global additive/
-multiplicative shift.
-
-## Contents
-
-- `ntc_clustered.h5ad` — **396,000 × 18,130** (gene-symbol `var_names`). `X` = log1p median-
-  normalized (no raw-counts layer retained; `obsm`/`layers`/`obsp`/`varm`/`varp` empty; `uns`
-  empty). `obs` (**17 columns**): `L0.8`, `PuroR`, `barcode`, `condition`, `donor`, `donor_id`,
-  `guide_group`, `guide_id`, `guide_type`, `lane_id`, `low_quality`, `n_genes_by_counts`,
-  `pct_counts_mt`, `perturbed_gene_id`, `perturbed_gene_name`, `top_guide_UMI_counts`,
-  `total_counts`. Coded donor/library IDs remain joinable to upstream public metadata — **coded,
-  not anonymous**. No donor demographics are included.
-- `stage01_umap_seed.json` — the 40,000-cell display overlay carrying **continuous program
-  scores** per cell (`treg_like_score`, `cd4_ctl_like_score` + `_actadj`, `th1_like_score`,
-  `th2_like_score`, `th17_like_score`, `tfh_like_score`, `th9_like_score`, `diff_*_score`) and a
-  display-only colour key (excluded from analysis).
+# spot Stage 1 — CD4 continuous transcriptional-program scores
+
+This repository contains the public data release for `spot` Stage 1,
+method version **`stage1-continuous-v3.0.1`**. It provides continuous RNA-program
+scores for a quota-balanced non-targeting-control (NTC) subset of the Marson
+GWCD4i primary-human-CD4 Perturb-seq dataset.
+
+The scores are measurements of specified transcriptional modules. They are not
+categorical cell-type, lineage, protein, cytotoxicity, or suppressive-function
+calls. The Stage-1 scoring and validation outputs contain no inferential p-values,
+q-values, or FDR estimates and do not report cell-type prevalence.
+
+This dataset repository deliberately contains **Stage 1 only**. Stage 2–4 result
+artifacts use additional sources and are not bundled here.
+
+## Source and subset
+
+Upstream public source:
+
+- **Primary Human CD4+ T Cell Perturb-seq**, CZI Virtual Cells Platform, v1.0,
+  released 22 December 2025:
+  <https://virtualcellmodels.cziscience.com/dataset/genome-scale-tcell-perturb-seq>
+- Zhu, Dann, et al., *Genome-scale perturb-seq in primary human CD4+ T cells maps
+  context-specific regulators of T cell programs and human immune traits*,
+  bioRxiv 2025.12.23.696273, <https://doi.org/10.64898/2025.12.23.696273>.
+- Authors' analysis repository:
+  <https://github.com/emdann/GWT_perturbseq_analysis_2025>.
+
+`ntc_clustered.h5ad` is a **spot-derived pinned input object**, not an original
+authors' release file. It contains 396,000 NTC cells: 33,000 cells from each of
+four coded donors in each of `Rest`, `Stim8hr`, and `Stim48hr`. This equal quota
+is a spot sampling decision and does not preserve the source population's
+condition proportions.
+
+The object is 396,000 × 18,130. Its `.X` matrix is already normalized to a
+per-cell target total of approximately 9,819 and `log1p` transformed. No raw
+counts layer is retained. Cluster metadata are retained, but latent and UMAP
+matrices are not stored in the H5AD (`obsm`, `obsp`, `layers`, and `uns` are
+empty). Frozen display coordinates are supplied separately.
+
+## Scoring method
+
+For cell `c` and program `p`:
+
+```text
+score(c, p) = mean(.X[c, measured panel genes])
+              - mean(.X[c, frozen expression-matched control genes])
+```
+
+The deterministic control construction is fully materialized in the release:
+
+- 25 expression bins computed over the pinned 396,000-cell matrix;
+- eligible pool = detected genes minus every program marker and activation
+  predictor marker;
+- program-order-invariant keyed SHA-256 selection;
+- 50 controls per occupied marker bin, without replacement;
+- master seed `12345`.
+
+There are 11 primary axes: Th1-like, Th2-like, Th17-like, Tfh-like, Treg-like,
+CD4 CTL-like, Th9-like, Naive, Activated, Memory, and Checkpoint. The
+activation-adjusted CD4 CTL-like residual is a sensitivity/display lane and is
+not a primary pole.
+
+Marker panels are curated canonical-marker panels with per-gene primary-source
+provenance in the registry. Masopust et al.,
+<https://doi.org/10.1038/s41577-025-01238-2>, is used as a nomenclature
+framework, not as the source of the marker panels.
+
+## Files
+
+| Path | Purpose |
+|---|---|
+| `ntc_clustered.h5ad` | Pinned 396,000-cell normalized NTC scoring source object. |
+| `stage1-continuous-v3.0.1/data/stage01_scores_full.parquet` | Authoritative 396,000 × 15 table: barcode, donor, condition, 11 primary scores, and one activation-adjusted sensitivity score. |
+| `stage1-continuous-v3.0.1/data/stage01_summary_v3.json` | Full-table program summaries by condition. |
+| `stage1-continuous-v3.0.1/data/stage01_umap_coordinates.json` | Frozen coordinates for the 40,000-cell display sample. |
+| `stage1-continuous-v3.0.1/data/stage01_umap_overlay_v3_hf.json` | The same 40,000 barcodes with v3 scores; display-only. |
+| `stage1-continuous-v3.0.1/method/` | Input identity, registry and marker provenance, frozen bins, controls, eligible pool, activation-association diagnostic, and Stage-2 scorer projection. |
+| `stage1-continuous-v3.0.1/validation/` | Frozen gate specification, descriptive validation, semantic amendment, constituent evidence, and non-gating diagnostics. |
+| `stage1-continuous-v3.0.1/contracts/` | Generic Stage-1 selection-contract schema. |
+| `stage1-continuous-v3.0.1/receipts/` | Independent reconstruction receipt. |
+| `MANIFEST.json` | Exact size and SHA-256 ledger for every current release file. |
+
+`stage01_stage2_registry_view.json` is only a Stage-1 scorer projection for
+downstream binding; it is not a Stage-2 result.
+
+## Validation status
+
+- Full-score raw SHA-256:
+  `de63b496e8121c77babe380e0c3b5ddfd66f9ce67d0d4e80f55645d177e27e5f`.
+- Canonical full-score content SHA-256:
+  `43c4296d5166740c334441a69df23bb440a073382bbe79628a3bb89e43d51316`.
+- The independent reconstruction receipt reports all checks passing, including
+  exact overlay-to-full score equality for all 40,000 display barcodes.
+- The 40,000-cell overlay is not the scientific analysis universe. An archived
+  representativeness diagnostic contains one failed overlay-distribution check;
+  use the full 396,000-cell table for analysis and summaries.
+- The frozen validation archive records that 0/33 program-condition pairs
+  cleared its prospective small-panel leave-one-marker robustness gate. That
+  result is retained for auditability, has `active_gate:false` in the current
+  selection contract, and is not a claim that the programs are biologically
+  invalid. Null/PENDING selectability fields inside the scorer registry are the
+  pre-validation snapshot; `stage01_selectability_v3.json` records the later
+  historical disposition.
+- `stage01_activation_association_v1.json` reports descriptive activation
+  association for every primary axis and the pooled activation-adjusted CTL
+  residual. Activation/timepoint association is not claimed to be removed.
+
+External-dataset confirmation and protein, lineage, and functional validation
+remain separate biological work; they are not implied by this scoring release.
+
+The HF overlay differs from the repository-generated overlay only in its
+top-level explanatory `note`. Cell records, coordinates, score fields, canonical
+score hash, and coordinate hash are unchanged. Both source and emitted raw hashes
+are recorded in `MANIFEST.json`; raw-byte reproduction is not claimed for that
+note-only packaging transform.
 
 ## Reproducibility
 
-`reproduce.sh` fetches this pinned revision + verifies the h5ad SHA-256, runs the deterministic
-continuous-score pipeline (`SEED=12345`, sorted control indices, `PYTHONHASHSEED=0`), and gates on
-a **per-barcode canonical-table hash** (not aggregate counts). Frozen reference:
-`n=40,000`; `canonical_table_sha256 = 6e1665d13eab1781407b43d232d089fb5fb6a6b9df5acd83cbbfb8fe3aed2755`;
-`barcode_set_sha256 = 1224312e52231f4b2e07c192b39c6f9c69dd6e2d5b8bd64d936c17a9b2435a93`.
-`ntc_clustered.h5ad` SHA-256 = `2edc6d318415c8b0ee779d707ab86e26ddb6f0274db51ab4a12f21ebfda50e43`.
+The pinned input identity is:
 
-## License & attribution
+- source HF revision:
+  `e5fcf98b56a9302921d402e97fc5a190bd88f9a6`;
+- `ntc_clustered.h5ad` raw SHA-256:
+  `2edc6d318415c8b0ee779d707ab86e26ddb6f0274db51ab4a12f21ebfda50e43`.
 
-Released under the **MIT License**, mirroring the upstream CZI dataset (its Croissant metadata
-declares MIT for all 12 AnnData splits). The upstream MIT copyright + permission notice is
-preserved verbatim in `NOTICE`. spot's transformations are separately MIT. Cite bioRxiv
-doi:10.64898/2025.12.23.696273. Upstream use is also subject to the CZI Acceptable Use Policy.
+Reproduction and verification code is in the public
+[`spot` repository](https://github.com/Kirit-Singh/spot/tree/29bd367b6e0ed674868041a4fe85d1f6fafd4cb8/01_programs/analysis).
+The input manifest, control algorithm, materialized controls/bins, validation
+constituents, and independent receipt are included here so the release can be
+audited without relying on moving branch names.
+
+## Privacy
+
+The H5AD contains coded donor, guide, lane, and library identifiers but no donor
+demographics. In particular, it does not include age, sex, ethnicity, weight,
+height, smoking status, blood type, or collection date. Coded identifiers may be
+joinable to upstream public metadata and therefore should not be described as
+anonymous. Release files were scanned for machine-local paths and credentials.
+
+## License and release history
+
+The official CZI dataset page declares the upstream dataset **MIT License**. The
+exact upstream copyright-holder notice is not supplied on that page, so this
+repository does not invent one. Spot-authored transformations and metadata are
+MIT licensed; see `LICENSE` and `NOTICE`.
+
+The historical v2 release is preserved at immutable commit
+`e5fcf98b56a9302921d402e97fc5a190bd88f9a6` and release tag
+`stage1-continuous-v2`. Its root `stage01_umap_seed.json` is intentionally absent
+from the current tree. v3.0.1 supersedes the earlier categorical-call,
+permutation-FDR, prevalence, paper-exact-embedding, and CP10k-equivalence claims;
+none of those claims is made by this release.
+
+Current release tag: **`stage1-continuous-v3.0.1`**.
 
-- Contact / issues: Kirit Singh (@KiritSingh).
-- Card version: **v2.0 (superseding, 2026-07)** — continuous-score remediation.

stage1-continuous-v3.0.1/contracts/spot.stage01_selection.v3.schema.json

@@ -0,0 +1,161 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$id": "spot.stage01_selection.v3",
+  "title": "Stage-1 generic research selection contract (v3)",
+  "description": "Emitted by stage2_bridge/emit_selection_contract.py for any supported (A program/direction, B program/direction, condition/mode). No production/research split and no 0-of-33 gating. Poles are ordered + separate; there is no combined objective (that is Stage-2's). The frozen selectability appears only as historical provenance (active_gate:false).",
+  "type": "object",
+  "additionalProperties": false,
+  "required": ["schema_version", "selection_origin", "execution_status", "analysis_mode", "estimator_id",
+               "estimator_status", "estimator", "selection_id", "selection_full_sha256", "question_id",
+               "canonical_content", "poles", "arms",
+               "trust_bindings", "provenance_bindings", "historical_validation_provenance",
+               "full_contract_content_sha256"],
+  "allOf": [
+    {"$comment": "ready requires an available estimator; a not_implemented estimator can never be ready",
+     "if": {"required": ["execution_status"], "properties": {"execution_status": {"const": "ready"}}},
+     "then": {"properties": {"estimator_status": {"const": "available"}}}},
+    {"$comment": "temporal_cross_condition + not_implemented must be awaiting_estimator",
+     "if": {"required": ["analysis_mode", "estimator_status"],
+            "properties": {"analysis_mode": {"const": "temporal_cross_condition"}, "estimator_status": {"const": "not_implemented"}}},
+     "then": {"properties": {"execution_status": {"const": "awaiting_estimator"}}}},
+    {"$comment": "the estimator must match the mode — a temporal mode may never borrow the within-condition estimator",
+     "if": {"required": ["analysis_mode"], "properties": {"analysis_mode": {"const": "within_condition"}}},
+     "then": {"properties": {"estimator_id": {"const": "within_condition_v1"}}}},
+    {"if": {"required": ["analysis_mode"], "properties": {"analysis_mode": {"const": "temporal_cross_condition"}}},
+     "then": {"properties": {"estimator_id": {"const": "temporal_cross_condition_v1"}}}}
+  ],
+  "properties": {
+    "schema_version": {"const": "spot.stage01_selection.v3"},
+    "selection_origin": {"enum": ["user_selected", "fixture"]},
+    "execution_status": {"enum": ["ready", "refused", "awaiting_estimator"]},
+    "analysis_mode": {"enum": ["within_condition", "temporal_cross_condition"]},
+    "estimator_id": {"enum": ["within_condition_v1", "temporal_cross_condition_v1"]},
+    "estimator_status": {"enum": ["available", "not_implemented"]},
+    "estimator": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["estimator_id", "analysis_mode", "n_conditions", "status"],
+      "properties": {
+        "estimator_id": {"enum": ["within_condition_v1", "temporal_cross_condition_v1"]},
+        "analysis_mode": {"enum": ["within_condition", "temporal_cross_condition"]},
+        "n_conditions": {"type": "integer", "minimum": 1, "maximum": 2},
+        "status": {"enum": ["available", "not_implemented"]},
+        "method_id": {"type": "string"},
+        "method_version": {"type": "string"},
+        "method_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+        "estimand_id": {"type": "string"},
+        "estimand_level": {"enum": ["population"]},
+        "estimand_is_per_cell_fate": {"const": false},
+        "inference_status": {"enum": ["not_calibrated"]}
+      }
+    },
+    "selection_id": {"type": "string", "pattern": "^[0-9a-f]{16}$"},
+    "selection_full_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+    "question_id": {"$comment": "biology-only ordered-question identity = sha256(canonical_json({A:{program_id,direction,condition:from}, B:{program_id,direction,condition:to}, analysis_mode}))[:16]; NO method/input binding, so it is stable across method/registry/source revisions (unlike selection_id).", "type": "string", "pattern": "^[0-9a-f]{16}$"},
+    "full_contract_content_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+    "canonical_content": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["A", "B", "analysis_mode", "combined_objective", "conditions", "dataset_id",
+                   "donor_scope", "effect_universe_id", "poles_separate", "registry_scorer_view_sha256",
+                   "source_h5ad_sha256", "source_hf_revision", "stage1_method_version"],
+      "properties": {
+        "A": {"$ref": "#/$defs/canonical_pole"},
+        "B": {"$ref": "#/$defs/canonical_pole"},
+        "analysis_mode": {"enum": ["within_condition", "temporal_cross_condition"]},
+        "combined_objective": {"type": "null"},
+        "conditions": {"type": "array", "minItems": 1, "maxItems": 2,
+                       "items": {"enum": ["Rest", "Stim8hr", "Stim48hr"]}},
+        "dataset_id": {"type": "string"},
+        "donor_scope": {"type": "string"},
+        "effect_universe_id": {"type": "string"},
+        "poles_separate": {"const": true},
+        "registry_scorer_view_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+        "source_h5ad_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+        "source_hf_revision": {"type": "string"},
+        "stage1_method_version": {"const": "stage1-continuous-v3.0.1"}
+      }
+    },
+    "poles": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["A", "B"],
+      "properties": {"A": {"$ref": "#/$defs/pole"}, "B": {"$ref": "#/$defs/pole"}}
+    },
+    "arms": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["away_from_A", "toward_B"],
+      "properties": {"away_from_A": {"$ref": "#/$defs/arm_ref"}, "toward_B": {"$ref": "#/$defs/arm_ref"}}
+    },
+    "trust_bindings": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["validation_raw_sha256", "validation_semantics_raw_sha256",
+                   "validation_semantics_self_canonical_sha256", "gate_spec_raw_sha256",
+                   "constituent_main_content_canonical_sha256", "constituent_overlay_donor_content_canonical_sha256",
+                   "marker_diagnostics_content_sha256", "scoring_view_raw_sha256", "scoring_view_canonical_sha256"],
+      "patternProperties": {"^[a-z0-9_]+$": {"type": "string", "pattern": "^[0-9a-f]{64}$"}}
+    },
+    "provenance_bindings": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["primary_registry_v3_raw_sha256"],
+      "properties": {"primary_registry_v3_raw_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"}}
+    },
+    "historical_validation_provenance": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["kind", "selectability_v3_raw_sha256", "active_gate"],
+      "properties": {
+        "kind": {"type": "string"},
+        "selectability_v3_raw_sha256": {"type": "string", "pattern": "^[0-9a-f]{64}$"},
+        "active_gate": {"const": false}
+      }
+    }
+  },
+  "$defs": {
+    "arm_ref": {
+      "$comment": "One independent reusable per-program arm (ROUND4_ADDENDUM c4773562). Keyed by desired_change (increase|decrease), NEVER pole_direction/role. pole_direction is selection metadata only. Keys: direct (program, desired_change, condition), pathway base (+ '|<source>'), temporal (program, desired_change, from, to) in temporal mode.",
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["role", "program_id", "pole_direction", "desired_change", "condition", "direct_arm_key", "pathway_arm_key_base"],
+      "properties": {
+        "role": {"enum": ["away_from_A", "toward_B"]},
+        "program_id": {"type": "string"},
+        "pole_direction": {"enum": ["high", "low"]},
+        "desired_change": {"enum": ["increase", "decrease"]},
+        "condition": {"enum": ["Rest", "Stim8hr", "Stim48hr"]},
+        "direct_arm_key": {"type": "string"},
+        "pathway_arm_key_base": {"type": "string"},
+        "temporal_arm_key": {"type": "string"}
+      }
+    },
+    "canonical_pole": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["program_id", "score_field", "direction"],
+      "properties": {
+        "program_id": {"type": "string"},
+        "score_field": {"type": "string"},
+        "direction": {"enum": ["high", "low"]}
+      }
+    },
+    "pole": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["program_id", "direction", "effect_projection_status", "n_measured",
+                   "n_panel_in_effect_universe", "n_control_in_effect_universe", "reason_codes"],
+      "properties": {
+        "program_id": {"type": "string"},
+        "direction": {"enum": ["high", "low"]},
+        "effect_projection_status": {"enum": ["available", "unavailable"]},
+        "n_measured": {"type": "integer", "minimum": 0},
+        "n_panel_in_effect_universe": {"type": "integer", "minimum": 0},
+        "n_control_in_effect_universe": {"type": "integer", "minimum": 0},
+        "reason_codes": {"type": "array",
+                         "items": {"enum": ["panel_below_effect_universe_min", "control_below_effect_universe_min"]}}
+      }
+    }
+  }
+}

stage01_umap_seed.json → stage1-continuous-v3.0.1/data/stage01_scores_full.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7f9dabd9eef74d65ff9d8008bbaf1e4456a832a9d1598c0d37e8e8632a5a9913
-size 26104050
+oid sha256:de63b496e8121c77babe380e0c3b5ddfd66f9ce67d0d4e80f55645d177e27e5f
+size 21872411

stage1-continuous-v3.0.1/data/stage01_summary_v3.json

@@ -0,0 +1,247 @@
+{
+ "schema": "spot.stage01_summary.v3",
+ "method_version": "stage1-continuous-v3.0.1",
+ "scoring_universe_n": 396000,
+ "by_program_condition": {
+  "th1_like_score": {
+   "Rest": {
+    "median": -0.53627,
+    "iqr": 0.47771,
+    "mad": 0.2378,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": -0.36302,
+    "iqr": 0.57546,
+    "mad": 0.28091,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": 0.23884,
+    "iqr": 0.86166,
+    "mad": 0.42903,
+    "n": 132000
+   }
+  },
+  "th2_like_score": {
+   "Rest": {
+    "median": -0.21407,
+    "iqr": 0.05269,
+    "mad": 0.02585,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": -0.0717,
+    "iqr": 0.49977,
+    "mad": 0.15826,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": -0.19241,
+    "iqr": 0.21579,
+    "mad": 0.0499,
+    "n": 132000
+   }
+  },
+  "th17_like_score": {
+   "Rest": {
+    "median": -0.00402,
+    "iqr": 0.00771,
+    "mad": 0.00402,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": -0.00618,
+    "iqr": 0.01092,
+    "mad": 0.00543,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": -0.0042,
+    "iqr": 0.00794,
+    "mad": 0.0042,
+    "n": 132000
+   }
+  },
+  "tfh_like_score": {
+   "Rest": {
+    "median": -0.06508,
+    "iqr": 0.03241,
+    "mad": 0.01612,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": -0.05427,
+    "iqr": 0.18611,
+    "mad": 0.03352,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": -0.06324,
+    "iqr": 0.12947,
+    "mad": 0.02509,
+    "n": 132000
+   }
+  },
+  "treg_like_score": {
+   "Rest": {
+    "median": -0.21712,
+    "iqr": 0.16953,
+    "mad": 0.05744,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": 0.03897,
+    "iqr": 0.36449,
+    "mad": 0.17968,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": 0.0152,
+    "iqr": 0.33109,
+    "mad": 0.16328,
+    "n": 132000
+   }
+  },
+  "cd4_ctl_like_score": {
+   "Rest": {
+    "median": -0.10868,
+    "iqr": 0.40414,
+    "mad": 0.19219,
+    "n": 132000
+   },
+   "Stim48hr": {
+    "median": 0.16747,
+    "iqr": 0.61966,
+    "mad": 0.30869,
+    "n": 132000
+   },
+   "Stim8hr": {
+    "median": 0.51968,
+    "iqr": 0.65436,
+    "mad": 0.32681,
+    "n": 132000
+   }
+  },
+  "th9_like_score": {
+   "Rest": {
+    "median": 0.0,
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stage1-continuous-v3.0.1/data/stage01_umap_coordinates.json

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stage1-continuous-v3.0.1/data/stage01_umap_overlay_v3_hf.json

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stage1-continuous-v3.0.1/method/stage01_activation_association_v1.json

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+  [
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+  [
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+  ],
+  [
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+  ],
+  [
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+  [
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+  [
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+  ]
+ ]
+}

stage1-continuous-v3.0.1/method/stage01_control_method.json

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+{
+  "schema": "spot.stage01_control_method.v1",
+  "method_version": "stage1-continuous-v3.0.1",
+  "scoring_method": "deterministic expression-bin-matched panel-minus-control score",
+  "score_formula": "score(c,p) = mean(.X over panel_genes_measured) - mean(.X over matched controls)",
+  "not_an_exact_scanpy_output": true,
+  "binning": {
+    "universe": "all 18130 finite assay-present genes (var_names), before pruning",
+    "statistic": "per-gene mean of .X over all 396000 cells (chunked float64 streaming column-sum)",
+    "rank": "scipy.stats.rankdata(mean_X, method='average'), 1-based",
+    "bin_formula": "floor((rank - 1) * 25 / n_finite), n_finite = 18130",
+    "range": [0, 24],
+    "n_bins": 25,
+    "n_mean_zero_genes_in_bin0": 174,
+    "bins_artifact": "stage01_bins_v3.csv",
+    "bins_artifact_raw_sha256": "5cf42fcdd6db26119ebde96f172dae12c8d5fe34b1202e34db1b586478a96fd8",
+    "bins_content_sha256": "32f926cace9322752aba10557b1bafe3e0c8f9d8f285551fcd2d3648bd335f78",
+    "bins_content_sha256_def": "sha256 of newline-joined 'var_index,gene,bin' rows in var_names order",
+    "bins_are_loaded_not_recomputed": "validation and the 20-seed sensitivity LOAD stage01_bins_v3.csv; the per-gene bins are NOT re-derived (the mean is float-order fragile on non-marker borderline genes)",
+    "superseded_intermediate": {
+      "bins_sha256": "0e8423df26d73c81751609f2e7041dada15db4c32938c40be77661c88f0d56d6",
+      "status": "unrecoverable — the Phase-1 kernel state that produced it is gone; the checkpoint stored only marker_bins/candidate_counts/hash, not the 18130 per-gene bins. NO per-gene diff can be claimed against it."
+    }
+  },
+  "bins_amendment": {
+    "revision": "stage1-continuous-v3.0.1",
+    "kind": "prospective equivalent-method amendment (NOT recovery of the original intermediate)",
+    "reason": "T7b self-check found bins_sha256=0e8423df not reproducible (float summation order); materialize the bins as an explicit committed artifact loaded (not recomputed) by validation.",
+    "scores_unchanged": "scorer coefficients and all 396k scores are byte-unchanged; no 396k re-run",
+    "acceptance_met": {
+      "marker_bins_match_checkpoint": true,
+      "occupied_bin_candidate_counts_match_checkpoint": true,
+      "all_2100_controls_reconstruct_byte_for_byte": true,
+      "note": "reproducing only the primary controls is necessary but not sufficient; (1)+(2)+(3) together prove equivalence on the occupied marker bins, so alt-seed draws reproduce"
+    },
+    "independent_verification": "lead loaded the emitted bins and confirmed all three acceptance checks with own code (marker_bins 0 mismatches, candidate_counts 0 mismatches, 2100 controls 0 mismatches; detected 17956, eligible 17903)",
+    "aborted_t7b_attempt": "the first T7b run correctly aborted (EXIT=1) on the bins_sha256 self-check; that abort triggered this amendment and is preserved in provenance (not silently replaced)"
+  },
+  "pool": {
+    "assay_present": 18130,
+    "detected_in_396k": 17956,
+    "control_eligible_pool": 17903,
+    "definition": "detected_in_396k minus the 53 present program/activation marker genes",
+    "activation_predictor_markers": ["CD69", "CD38", "MKI67", "TNFRSF9", "IL2RA"],
+    "pool_sha256": "72b4648c96588eae57eb6ff25ca9d8717f19c14549c9f1f93640dc2aaa11b5db"
+  },
+  "draw": {
+    "scheme": "keyed_sha256",
+    "key": "12345|{program_id}|{bin}|{gene}",
+    "encoding": "utf-8",
+    "select": "50 lowest hex digests per occupied marker bin, no replacement",
+    "digest_tie": "digest_hex ascending, then var_name index ascending",
+    "ctrl_size": 50,
+    "occupied_bin_definition": "bins containing the program's detected (measured) panel genes"
+  },
+  "activation_predictor_draw": {
+    "program_id": "activation_predictor",
+    "panel": ["CD69", "CD38", "MKI67", "TNFRSF9", "IL2RA"],
+    "occupied_bins": [18, 22, 24],
+    "n_controls": 150,
+    "leakage": 0,
+    "materialized": true,
+    "independently_verified": "lead reproduced these 150 rows with the frozen algorithm (key 12345|activation_predictor|{bin}|{gene}); occupied bins {18,22,24}, zero leakage",
+    "note": "controls for the activation-adjusted CD4 CTL-like sensitivity lane; display/sensitivity-only; never a Stage-2 pole. Rows are in stage01_controls_v3.csv (program_id=activation_predictor)."
+  },
+  "present_but_undetected_panel_genes": [],
+  "intended_only_absent": [
+    {"symbol": "HLA-DRA", "ensembl": "ENSG00000204287", "program": "diff_activated", "note": "absent from var; recorded intended-only; never scored"}
+  ],
+  "controls_table": "stage01_controls_v3.csv",
+  "cross_program_overlap": {"max_shared": 13, "max_pair": ["treg_like", "th2_like"], "mean_shared": 2.33, "distinct_control_genes": 1828, "total_draws": 1950},
+  "residual_correlation_note": "program-order-invariant draws remove DIRECT cross-panel leakage; they do NOT make programs biologically or statistically independent. Shared controls and genuine co-expression can still correlate programs; residual correlation is measured and reported in validation, never asserted away.",
+  "independent_verification": {
+    "verifier": "lead (generator != verifier)",
+    "method": "independent code: chunked float64 CSR column-means -> divN bins -> detected pool -> own keyed-hash draws",
+    "result": "11/11 primary programs byte-identical control sets (1950 rows, 0 mismatches on (program_id,bin,rank_in_bin)) + activation_predictor 150 rows independently reproduced (bins {18,22,24}, 0 leakage); total 2100 control rows; reproduced detected=17956, control_eligible_pool=17903, bin24_eligible=715, bin0_eligible=552, marker union 54 present 53 absent [HLA-DRA]"
+  },
+  "no_p_or_fdr": true
+}

stage1-continuous-v3.0.1/method/stage01_controls_v3.csv

@@ -0,0 +1,2101 @@
+program_id,bin,rank_in_bin,control_symbol
+diff_naive,16,0,PLOD3
+diff_naive,16,1,FKBP8
+diff_naive,16,2,ASPHD2
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+diff_naive,16,4,UBXN2A
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+diff_naive,16,8,KIF18B
+diff_naive,16,9,LTBP3
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+diff_naive,16,12,ZSWIM7
+diff_naive,16,13,TRIM4
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+diff_naive,16,15,ERCC2
+diff_naive,16,16,HEG1
+diff_naive,16,17,ZC3HC1
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+diff_naive,16,20,ATG9A
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+diff_naive,16,22,SCYL3
+diff_naive,16,23,PLP2
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+diff_naive,17,23,GAB2
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+diff_naive,17,28,TSPAN3
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+diff_naive,17,31,KCTD17
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+diff_naive,17,39,SMIM20
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+diff_naive,17,47,GTPBP10
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+diff_naive,17,49,ANKRD13B
+diff_naive,22,0,ERH
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+diff_naive,22,11,BCL11B
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+diff_naive,24,31,BIRC3
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+diff_naive,24,33,MAPKAPK2
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+diff_naive,24,35,IL2RB
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+diff_naive,24,47,MAPK6
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+diff_activated,18,0,DCAF1
+diff_activated,18,1,PLD6
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+cd4_ctl_like,9,39,HDC
+cd4_ctl_like,9,40,ZNF555
+cd4_ctl_like,9,41,MYO1A
+cd4_ctl_like,9,42,WNT7A
+cd4_ctl_like,9,43,KIAA1522
+cd4_ctl_like,9,44,FAM167B
+cd4_ctl_like,9,45,SLC25A34
+cd4_ctl_like,9,46,XKR9
+cd4_ctl_like,9,47,SLC34A1
+cd4_ctl_like,9,48,ZNF572
+cd4_ctl_like,9,49,NIPAL2
+cd4_ctl_like,13,0,ZNF383
+cd4_ctl_like,13,1,BEND5
+cd4_ctl_like,13,2,SGPP2
+cd4_ctl_like,13,3,ENSG00000284691
+cd4_ctl_like,13,4,TLK2
+cd4_ctl_like,13,5,PHEX
+cd4_ctl_like,13,6,RPP25
+cd4_ctl_like,13,7,IPCEF1
+cd4_ctl_like,13,8,PPP1R3F
+cd4_ctl_like,13,9,ALG14
+cd4_ctl_like,13,10,KAT2A
+cd4_ctl_like,13,11,PLXNA4
+cd4_ctl_like,13,12,SH2D3A
+cd4_ctl_like,13,13,SMAD5
+cd4_ctl_like,13,14,ZNF445
+cd4_ctl_like,13,15,ST20
+cd4_ctl_like,13,16,BCLAF3
+cd4_ctl_like,13,17,VILL
+cd4_ctl_like,13,18,HMGN5
+cd4_ctl_like,13,19,EVA1B
+cd4_ctl_like,13,20,B4GAT1
+cd4_ctl_like,13,21,ZNF133
+cd4_ctl_like,13,22,KPTN
+cd4_ctl_like,13,23,KBTBD3
+cd4_ctl_like,13,24,NT5M
+cd4_ctl_like,13,25,SLC30A4
+cd4_ctl_like,13,26,TMEM203
+cd4_ctl_like,13,27,BLVRB
+cd4_ctl_like,13,28,RYK
+cd4_ctl_like,13,29,LIN52
+cd4_ctl_like,13,30,RAC3
+cd4_ctl_like,13,31,TAF6L
+cd4_ctl_like,13,32,TEDC2
+cd4_ctl_like,13,33,SLC25A13
+cd4_ctl_like,13,34,PHOSPHO2
+cd4_ctl_like,13,35,PHC1
+cd4_ctl_like,13,36,FARS2
+cd4_ctl_like,13,37,PPARG
+cd4_ctl_like,13,38,GRAMD2B
+cd4_ctl_like,13,39,ATP5PF
+cd4_ctl_like,13,40,DIXDC1
+cd4_ctl_like,13,41,COQ8B
+cd4_ctl_like,13,42,GPAM
+cd4_ctl_like,13,43,SEMA4B
+cd4_ctl_like,13,44,GSTA4
+cd4_ctl_like,13,45,RGS2
+cd4_ctl_like,13,46,DHRS7B
+cd4_ctl_like,13,47,ZNF211
+cd4_ctl_like,13,48,DXO
+cd4_ctl_like,13,49,MSS51
+cd4_ctl_like,16,0,ALKBH3
+cd4_ctl_like,16,1,RPN2
+cd4_ctl_like,16,2,HMBOX1
+cd4_ctl_like,16,3,PDSS2
+cd4_ctl_like,16,4,PAAF1
+cd4_ctl_like,16,5,GATD1
+cd4_ctl_like,16,6,SHMT1
+cd4_ctl_like,16,7,CCDC174
+cd4_ctl_like,16,8,MAFG
+cd4_ctl_like,16,9,UBE2H
+cd4_ctl_like,16,10,EXT1
+cd4_ctl_like,16,11,PRUNE1
+cd4_ctl_like,16,12,ST3GAL3
+cd4_ctl_like,16,13,ARSA
+cd4_ctl_like,16,14,INTS1
+cd4_ctl_like,16,15,DCAF6
+cd4_ctl_like,16,16,ZMYM5
+cd4_ctl_like,16,17,GRPEL2
+cd4_ctl_like,16,18,SMYD5
+cd4_ctl_like,16,19,BRF2
+cd4_ctl_like,16,20,C19orf47
+cd4_ctl_like,16,21,PHKG2
+cd4_ctl_like,16,22,ANAPC2
+cd4_ctl_like,16,23,THAP7
+cd4_ctl_like,16,24,BBX
+cd4_ctl_like,16,25,CMC1
+cd4_ctl_like,16,26,PSME3IP1
+cd4_ctl_like,16,27,MTMR10
+cd4_ctl_like,16,28,CAMK2G
+cd4_ctl_like,16,29,NAA50
+cd4_ctl_like,16,30,KIAA0586
+cd4_ctl_like,16,31,ALKBH7
+cd4_ctl_like,16,32,CCDC86
+cd4_ctl_like,16,33,FAM199X
+cd4_ctl_like,16,34,LGALS3BP
+cd4_ctl_like,16,35,SCYL3
+cd4_ctl_like,16,36,METTL14
+cd4_ctl_like,16,37,EID2
+cd4_ctl_like,16,38,NEK6
+cd4_ctl_like,16,39,JMJD4
+cd4_ctl_like,16,40,TXK
+cd4_ctl_like,16,41,TOP3B
+cd4_ctl_like,16,42,GLIPR1
+cd4_ctl_like,16,43,PCMTD2
+cd4_ctl_like,16,44,CDYL
+cd4_ctl_like,16,45,KIAA0408
+cd4_ctl_like,16,46,ARID4A
+cd4_ctl_like,16,47,ZNF263
+cd4_ctl_like,16,48,MTAP
+cd4_ctl_like,16,49,TBCEL
+cd4_ctl_like,23,0,NCAPD2
+cd4_ctl_like,23,1,RUNX3
+cd4_ctl_like,23,2,VPS26A
+cd4_ctl_like,23,3,NFE2L2
+cd4_ctl_like,23,4,DEGS1
+cd4_ctl_like,23,5,APEX1
+cd4_ctl_like,23,6,STIM1
+cd4_ctl_like,23,7,DAXX
+cd4_ctl_like,23,8,CCNC
+cd4_ctl_like,23,9,NCOA3
+cd4_ctl_like,23,10,DNTTIP2
+cd4_ctl_like,23,11,NCOA4
+cd4_ctl_like,23,12,EHBP1L1
+cd4_ctl_like,23,13,PNISR
+cd4_ctl_like,23,14,CHD4
+cd4_ctl_like,23,15,PPP1R12A
+cd4_ctl_like,23,16,EXOSC8
+cd4_ctl_like,23,17,HPRT1
+cd4_ctl_like,23,18,PPP2R2A
+cd4_ctl_like,23,19,CHMP5
+cd4_ctl_like,23,20,TMA7
+cd4_ctl_like,23,21,PHF10
+cd4_ctl_like,23,22,SRSF4
+cd4_ctl_like,23,23,SMG5
+cd4_ctl_like,23,24,RUVBL1
+cd4_ctl_like,23,25,STX16
+cd4_ctl_like,23,26,OGT
+cd4_ctl_like,23,27,RFLNB
+cd4_ctl_like,23,28,TGFBR1
+cd4_ctl_like,23,29,ADAM10
+cd4_ctl_like,23,30,HSF1
+cd4_ctl_like,23,31,PDE7A
+cd4_ctl_like,23,32,BBLN
+cd4_ctl_like,23,33,DNMT1
+cd4_ctl_like,23,34,ANKHD1
+cd4_ctl_like,23,35,TOB1
+cd4_ctl_like,23,36,RTN3
+cd4_ctl_like,23,37,PCM1
+cd4_ctl_like,23,38,NSA2
+cd4_ctl_like,23,39,BCL3
+cd4_ctl_like,23,40,MAT2A
+cd4_ctl_like,23,41,ARHGAP25
+cd4_ctl_like,23,42,ANAPC5
+cd4_ctl_like,23,43,ENOPH1
+cd4_ctl_like,23,44,ZFP36L2
+cd4_ctl_like,23,45,SH3BP1
+cd4_ctl_like,23,46,PCMT1
+cd4_ctl_like,23,47,PUF60
+cd4_ctl_like,23,48,PRPF31
+cd4_ctl_like,23,49,NUMA1
+cd4_ctl_like,24,0,EDF1
+cd4_ctl_like,24,1,RCSD1
+cd4_ctl_like,24,2,PAK2
+cd4_ctl_like,24,3,CD3D
+cd4_ctl_like,24,4,CD7
+cd4_ctl_like,24,5,CYBA
+cd4_ctl_like,24,6,COX16
+cd4_ctl_like,24,7,SPTAN1
+cd4_ctl_like,24,8,USF2
+cd4_ctl_like,24,9,HECA
+cd4_ctl_like,24,10,CDC42SE2
+cd4_ctl_like,24,11,SDF4
+cd4_ctl_like,24,12,EFHD2
+cd4_ctl_like,24,13,SLC39A8
+cd4_ctl_like,24,14,TMEM106C
+cd4_ctl_like,24,15,DGKA
+cd4_ctl_like,24,16,NOP53
+cd4_ctl_like,24,17,HNRNPH3
+cd4_ctl_like,24,18,LCK
+cd4_ctl_like,24,19,IER5
+cd4_ctl_like,24,20,RASSF5
+cd4_ctl_like,24,21,CLDND1
+cd4_ctl_like,24,22,LCP1
+cd4_ctl_like,24,23,UCP2
+cd4_ctl_like,24,24,LRRN3
+cd4_ctl_like,24,25,SOCS1
+cd4_ctl_like,24,26,EIF4A2
+cd4_ctl_like,24,27,SNRPB2
+cd4_ctl_like,24,28,RPA1
+cd4_ctl_like,24,29,GNB2
+cd4_ctl_like,24,30,SF3B3
+cd4_ctl_like,24,31,NFKB2
+cd4_ctl_like,24,32,ATP5PB
+cd4_ctl_like,24,33,TOP1
+cd4_ctl_like,24,34,CERS2
+cd4_ctl_like,24,35,SEC11C
+cd4_ctl_like,24,36,HAPSTR1
+cd4_ctl_like,24,37,FAM32A
+cd4_ctl_like,24,38,FIS1
+cd4_ctl_like,24,39,LYAR
+cd4_ctl_like,24,40,TNFRSF1B
+cd4_ctl_like,24,41,JAK3
+cd4_ctl_like,24,42,ARF6
+cd4_ctl_like,24,43,EZR
+cd4_ctl_like,24,44,CREM
+cd4_ctl_like,24,45,MAP7D1
+cd4_ctl_like,24,46,ELL2
+cd4_ctl_like,24,47,ARHGAP15
+cd4_ctl_like,24,48,CD5
+cd4_ctl_like,24,49,MYDGF
+th1_like,21,0,APOL1
+th1_like,21,1,NBEAL2
+th1_like,21,2,PNRC1
+th1_like,21,3,GABPA
+th1_like,21,4,SNX4
+th1_like,21,5,LARP4B
+th1_like,21,6,PTGER4
+th1_like,21,7,TNPO3
+th1_like,21,8,GPN3
+th1_like,21,9,PCSK7
+th1_like,21,10,NCAPG
+th1_like,21,11,RMC1
+th1_like,21,12,GRAP2
+th1_like,21,13,RBM42
+th1_like,21,14,RAB4A
+th1_like,21,15,RUFY1
+th1_like,21,16,NFAT5
+th1_like,21,17,ATP5F1D
+th1_like,21,18,FOXN2
+th1_like,21,19,CBX5
+th1_like,21,20,TM7SF3
+th1_like,21,21,HDDC3
+th1_like,21,22,TRAF4
+th1_like,21,23,UGGT1
+th1_like,21,24,ACOT9
+th1_like,21,25,BCL2A1
+th1_like,21,26,PRPF4
+th1_like,21,27,ZWINT
+th1_like,21,28,PNO1
+th1_like,21,29,INTS15
+th1_like,21,30,GBP4
+th1_like,21,31,SETD1B
+th1_like,21,32,LASP1
+th1_like,21,33,PSMD8
+th1_like,21,34,PQBP1
+th1_like,21,35,RAB11A
+th1_like,21,36,DECR1
+th1_like,21,37,HAX1
+th1_like,21,38,NDUFS7
+th1_like,21,39,POLR2L
+th1_like,21,40,ATRX
+th1_like,21,41,MAP3K7
+th1_like,21,42,ZFAND1
+th1_like,21,43,RFTN1
+th1_like,21,44,FXN
+th1_like,21,45,AHI1
+th1_like,21,46,USP39
+th1_like,21,47,IMP3
+th1_like,21,48,TNPO2
+th1_like,21,49,TPD52L2
+th1_like,23,0,BTF3L4
+th1_like,23,1,NCAPD2
+th1_like,23,2,PMAIP1
+th1_like,23,3,UBE2S
+th1_like,23,4,ELOB
+th1_like,23,5,UBA2
+th1_like,23,6,NDUFB10
+th1_like,23,7,ZMAT2
+th1_like,23,8,TP53
+th1_like,23,9,EXOSC8
+th1_like,23,10,PRPF31
+th1_like,23,11,NOP10
+th1_like,23,12,METTL9
+th1_like,23,13,DGUOK
+th1_like,23,14,PRPF38B
+th1_like,23,15,RHOF
+th1_like,23,16,MLF2
+th1_like,23,17,ATP2A2
+th1_like,23,18,DCTD
+th1_like,23,19,CHD2
+th1_like,23,20,PSMD9
+th1_like,23,21,WAS
+th1_like,23,22,CTDSP1
+th1_like,23,23,TNIP2
+th1_like,23,24,NDUFB5
+th1_like,23,25,SMAD3
+th1_like,23,26,PNN
+th1_like,23,27,TPX2
+th1_like,23,28,HGS
+th1_like,23,29,NEMF
+th1_like,23,30,SMARCA4
+th1_like,23,31,KAT2B
+th1_like,23,32,AKT1
+th1_like,23,33,METTL26
+th1_like,23,34,BNIP2
+th1_like,23,35,IQGAP2
+th1_like,23,36,METTL5
+th1_like,23,37,SMARCB1
+th1_like,23,38,TOP2A
+th1_like,23,39,SELENOK
+th1_like,23,40,RNF167
+th1_like,23,41,IMPDH2
+th1_like,23,42,UBE4A
+th1_like,23,43,MAP4K1
+th1_like,23,44,FASN
+th1_like,23,45,AP1M1
+th1_like,23,46,GLUL
+th1_like,23,47,MAP2K2
+th1_like,23,48,CMC2
+th1_like,23,49,CASC3
+th1_like,24,0,STAG2
+th1_like,24,1,CGGBP1
+th1_like,24,2,CBX3
+th1_like,24,3,MLLT6
+th1_like,24,4,UBE2R2
+th1_like,24,5,IRF4
+th1_like,24,6,ATP5MG
+th1_like,24,7,HMGB2
+th1_like,24,8,ARPC4
+th1_like,24,9,MDM4
+th1_like,24,10,SUN2
+th1_like,24,11,MBD2
+th1_like,24,12,TMSB10
+th1_like,24,13,C11orf58
+th1_like,24,14,EBNA1BP2
+th1_like,24,15,TMEM50A
+th1_like,24,16,SMS
+th1_like,24,17,TMEM33
+th1_like,24,18,SNU13
+th1_like,24,19,LGALS1
+th1_like,24,20,TMSB4X
+th1_like,24,21,EIF3B
+th1_like,24,22,GTF2A2
+th1_like,24,23,VDAC3
+th1_like,24,24,S100A11
+th1_like,24,25,NCL
+th1_like,24,26,NME1
+th1_like,24,27,TUT7
+th1_like,24,28,AIMP1
+th1_like,24,29,ZC3HAV1
+th1_like,24,30,UFM1
+th1_like,24,31,SRSF2
+th1_like,24,32,CD40LG
+th1_like,24,33,CYTH1
+th1_like,24,34,S100A6
+th1_like,24,35,BAG6
+th1_like,24,36,ANAPC11
+th1_like,24,37,HECA
+th1_like,24,38,UCP2
+th1_like,24,39,OSTF1
+th1_like,24,40,SEPTIN1
+th1_like,24,41,PSMA2
+th1_like,24,42,MT-ND3
+th1_like,24,43,CD28
+th1_like,24,44,ANXA2
+th1_like,24,45,CAPZA1
+th1_like,24,46,BRD2
+th1_like,24,47,ZNF644
+th1_like,24,48,CYBA
+th1_like,24,49,NUDT5
+th2_like,9,0,BEST4
+th2_like,9,1,ADAMTS4
+th2_like,9,2,RPH3AL
+th2_like,9,3,GAL
+th2_like,9,4,CILP2
+th2_like,9,5,ASAP2
+th2_like,9,6,ETV7
+th2_like,9,7,CCER2
+th2_like,9,8,C2orf66
+th2_like,9,9,PITX1
+th2_like,9,10,ITGA7
+th2_like,9,11,DENND2B
+th2_like,9,12,CCDC153
+th2_like,9,13,NCF1
+th2_like,9,14,SCN8A
+th2_like,9,15,NOS3
+th2_like,9,16,SRRM5
+th2_like,9,17,CAMK2N2
+th2_like,9,18,ZNF695
+th2_like,9,19,THNSL2
+th2_like,9,20,GPD1
+th2_like,9,21,NT5C1A
+th2_like,9,22,LIPH
+th2_like,9,23,RNF217
+th2_like,9,24,GLDC
+th2_like,9,25,LRG1
+th2_like,9,26,WWTR1
+th2_like,9,27,KRT18
+th2_like,9,28,CRIP2
+th2_like,9,29,PPM1N
+th2_like,9,30,HBQ1
+th2_like,9,31,GREM2
+th2_like,9,32,NMU
+th2_like,9,33,PRKAR2B
+th2_like,9,34,NYAP1
+th2_like,9,35,DUSP29
+th2_like,9,36,NRSN2
+th2_like,9,37,DOC2A
+th2_like,9,38,PTPRF
+th2_like,9,39,RHBDL1
+th2_like,9,40,HNF1B
+th2_like,9,41,MC1R
+th2_like,9,42,TPBGL
+th2_like,9,43,GK3
+th2_like,9,44,COL5A2
+th2_like,9,45,SPTBN5
+th2_like,9,46,DCAF4L1
+th2_like,9,47,EPHB4
+th2_like,9,48,HAL
+th2_like,9,49,ADAMTSL5
+th2_like,12,0,CKB
+th2_like,12,1,TP53I3
+th2_like,12,2,CLK2
+th2_like,12,3,CKAP4
+th2_like,12,4,GCNA
+th2_like,12,5,SULT1B1
+th2_like,12,6,ERP27
+th2_like,12,7,SCN9A
+th2_like,12,8,ZNF699
+th2_like,12,9,DCBLD2
+th2_like,12,10,LIN7A
+th2_like,12,11,AK9
+th2_like,12,12,KIAA1191
+th2_like,12,13,RAB30
+th2_like,12,14,RNF122
+th2_like,12,15,ZSWIM3
+th2_like,12,16,RNF130
+th2_like,12,17,SANBR
+th2_like,12,18,CYB561
+th2_like,12,19,ID3
+th2_like,12,20,GM2A
+th2_like,12,21,IL22
+th2_like,12,22,WDR19
+th2_like,12,23,TMCC1
+th2_like,12,24,EPM2A
+th2_like,12,25,EPHX2
+th2_like,12,26,MBD5
+th2_like,12,27,FCER1G
+th2_like,12,28,LTO1
+th2_like,12,29,ZNF17
+th2_like,12,30,FAM114A1
+th2_like,12,31,FSD1
+th2_like,12,32,ZNF235
+th2_like,12,33,CHST10
+th2_like,12,34,FSD1L
+th2_like,12,35,ZKSCAN3
+th2_like,12,36,IFT122
+th2_like,12,37,ASB13
+th2_like,12,38,BPHL
+th2_like,12,39,CEACAM1
+th2_like,12,40,FCGRT
+th2_like,12,41,KIF27
+th2_like,12,42,ZNF821
+th2_like,12,43,VPS9D1
+th2_like,12,44,CPNE8
+th2_like,12,45,ZFP69B
+th2_like,12,46,PLEKHA1
+th2_like,12,47,ZNF585B
+th2_like,12,48,ZNF606
+th2_like,12,49,TRIO
+th2_like,21,0,TMEM126A
+th2_like,21,1,TMED7
+th2_like,21,2,TFAM
+th2_like,21,3,TAOK3
+th2_like,21,4,ACAA1
+th2_like,21,5,NPC2
+th2_like,21,6,SLC5A3
+th2_like,21,7,FOXO1
+th2_like,21,8,SNAPC3
+th2_like,21,9,PTAR1
+th2_like,21,10,AURKAIP1
+th2_like,21,11,TENT2
+th2_like,21,12,IRF9
+th2_like,21,13,AIMP2
+th2_like,21,14,TERF2
+th2_like,21,15,SH3BP5
+th2_like,21,16,PRIM1
+th2_like,21,17,FUS
+th2_like,21,18,TNIK
+th2_like,21,19,PRRC2A
+th2_like,21,20,ICAM2
+th2_like,21,21,PURB
+th2_like,21,22,YTHDF3
+th2_like,21,23,FOXK2
+th2_like,21,24,CCDC12
+th2_like,21,25,N4BP2
+th2_like,21,26,CEBPZOS
+th2_like,21,27,MED8
+th2_like,21,28,PLSCR3
+th2_like,21,29,AFG3L2
+th2_like,21,30,ATG5
+th2_like,21,31,CENPH
+th2_like,21,32,RIN3
+th2_like,21,33,YJU2
+th2_like,21,34,SF3B1
+th2_like,21,35,SEC14L1
+th2_like,21,36,NKTR
+th2_like,21,37,P2RY8
+th2_like,21,38,HK2
+th2_like,21,39,ZNF655
+th2_like,21,40,IKBKG
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+activation_predictor,24,22,PRRC2C
+activation_predictor,24,23,HNRNPAB
+activation_predictor,24,24,RAP1A
+activation_predictor,24,25,ICOS
+activation_predictor,24,26,SEPTIN6
+activation_predictor,24,27,MDFIC
+activation_predictor,24,28,COX6A1
+activation_predictor,24,29,ARHGDIA
+activation_predictor,24,30,NFKBIA
+activation_predictor,24,31,CDK6
+activation_predictor,24,32,BHLHE40
+activation_predictor,24,33,FAM32A
+activation_predictor,24,34,U2SURP
+activation_predictor,24,35,MAF1
+activation_predictor,24,36,PTPRC
+activation_predictor,24,37,CLDND1
+activation_predictor,24,38,SH3BGRL3
+activation_predictor,24,39,DEK
+activation_predictor,24,40,PPP1R9B
+activation_predictor,24,41,BIRC3
+activation_predictor,24,42,AGO2
+activation_predictor,24,43,TAP2
+activation_predictor,24,44,EID1
+activation_predictor,24,45,ELAVL1
+activation_predictor,24,46,RYBP
+activation_predictor,24,47,TANK
+activation_predictor,24,48,TFRC
+activation_predictor,24,49,RNF7

stage1-continuous-v3.0.1/method/stage01_input_manifest.json

@@ -0,0 +1,35 @@
+{
+  "schema": "spot.stage01_input_manifest.v1",
+  "method_version": "stage1-continuous-v3.0.1",
+  "input_object": "ntc_clustered.h5ad",
+  "hf_source": "KiritSingh/spot-CD4-Marson",
+  "hf_revision": "e5fcf98b56a9302921d402e97fc5a190bd88f9a6",
+  "raw_file_sha256": "2edc6d318415c8b0ee779d707ab86e26ddb6f0274db51ab4a12f21ebfda50e43",
+  "authoritative_identity": "raw_file_sha256 (byte-exact; matches the committed v2 H5AD_SHA). This is the ONLY current verified identity check.",
+  "canonical_content_sha256_archived_diagnostic": {
+    "value": "4ba50ccdf759115297b92bdfb7ad65c5c952b84093314245d21fe9af19d0f714",
+    "status": "ARCHIVED Phase-1 diagnostic — NOT a current verified hash. Its canonicalization algorithm is not fully specified and was not independently reproduced this session; do not present it as verified merely because Phase-1 emitted it. The raw_file_sha256 is authoritative."
+  },
+  "var_order_sha256": "c53793d91022c1d756ee972b470734a29717ae5522af179d5f1fcad0dda0e49f",
+  "barcode_set_sha256": "53e647b39399cb052041c9ee416337a5ee0680752cf34537eed3bd4630af8cd7",
+  "identity_check": "raw_file_sha256 ONLY (byte-exact); NOT per-cell total equality, NOT the archived canonical",
+  "score_integrity_rule": "compare emitted 5-decimal scores to independently-recomputed scores AFTER applying the frozen round-to-5-decimals rule; prefer EXACT equality after canonical rounding. If a tolerance is retained it must be INCLUSIVE: abs_error <= 5e-6.",
+  "dims": {"n_cells": 396000, "n_genes": 18130, "nnz": 1642556122},
+  "storage": "CSR float32; no layers; no raw counts layer",
+  "design": {"donors": ["D1", "D2", "D3", "D4"], "conditions": ["Rest", "Stim8hr", "Stim48hr"], "per_donor_condition_quota": 33000},
+  "normalization": {
+    "scheme": ".X = median_total normalize + log1p",
+    "target_total": 9819,
+    "note": "target total 9819 with float roundoff",
+    "observed_reconstructed_per_cell_totals": {"min": 9818.9985536, "max": 9819.0017994, "median": 9819.0000498, "cells_exactly_float64_9819": 0, "n_cells": 396000},
+    "raw_layer_present": false,
+    "scores_computed_from": ".X (never described as 'from raw expression')"
+  },
+  "cp10k_reconstruction": {
+    "role": "archived SENSITIVITY only; never mixed with or equated to the primary median-normalized scores",
+    "recipe": "expm1(.X) -> per-cell L1 renormalize to target 1e4 -> log1p",
+    "status": "recipe finalized at the CP10k descriptive sensitivity (Task 7b)"
+  },
+  "independently_verified": true,
+  "verification_note": "lead independently re-derived dims (396000x18130), detected_in_396k=17956, n mean==0=174, control_eligible_pool=17903 from the raw CSR (chunked float64 column means)"
+}

stage1-continuous-v3.0.1/method/stage01_stage2_registry_view.json

@@ -0,0 +1,4095 @@
+{
+ "schema_version": "spot.stage01_stage2_registry_view.v1",
+ "method_version": "stage1-continuous-v3.0.1",
+ "view_kind": "executable_scorer_projection",
+ "note": "Executable scorer projection of the primary v3 registry into the Stage-2 effect-universe gene space. Citation/rationale/provenance are intentionally excluded so this hash is invariant to provenance-only edits. panel_ensembl/control_ensembl carry ONLY symbols present in the effect universe; retained/missing lists are explicit. No value recomputed.",
+ "effect_universe_id": "marson2025_gwcd4_perturbseq : GWCD4i.DE_stats.h5ad",
+ "effect_universe_symbols_sha256": "10ba3c630c867d923745d4956946a06eb14959d345163dcf2d5d49e217faf826",
+ "effect_universe_n_symbols": 10282,
+ "n_programs": 11,
+ "sensitivity_lane_excluded": [
+  "cd4_ctl_like_actadj"
+ ],
+ "programs": [
+  {
+   "program_id": "th1_like",
+   "score_field": "th1_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.25,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 4,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "CXCR3",
+    "TBX21",
+    "IFNG",
+    "IL12RB2"
+   ],
+   "panel_symbols_retained": [
+    "CXCR3",
+    "TBX21",
+    "IFNG",
+    "IL12RB2"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 4,
+   "n_panel_in_effect_universe": 4,
+   "panel_ensembl": [
+    "ENSG00000186810",
+    "ENSG00000073861",
+    "ENSG00000111537",
+    "ENSG00000081985"
+   ],
+   "control_symbols_retained": [
+    "APOL1",
+    "NBEAL2",
+    "PNRC1",
+    "GABPA",
+    "SNX4",
+    "LARP4B",
+    "PTGER4",
+    "TNPO3",
+    "PCSK7",
+    "RMC1",
+    "GRAP2",
+    "RBM42",
+    "RAB4A",
+    "RUFY1",
+    "NFAT5",
+    "ATP5F1D",
+    "FOXN2",
+    "CBX5",
+    "TM7SF3",
+    "HDDC3",
+    "TRAF4",
+    "UGGT1",
+    "ACOT9",
+    "BCL2A1",
+    "ZWINT",
+    "PNO1",
+    "INTS15",
+    "GBP4",
+    "SETD1B",
+    "LASP1",
+    "PSMD8",
+    "PQBP1",
+    "RAB11A",
+    "DECR1",
+    "HAX1",
+    "NDUFS7",
+    "POLR2L",
+    "ATRX",
+    "MAP3K7",
+    "ZFAND1",
+    "RFTN1",
+    "FXN",
+    "AHI1",
+    "USP39",
+    "TNPO2",
+    "TPD52L2",
+    "BTF3L4",
+    "NCAPD2",
+    "PMAIP1",
+    "UBE2S",
+    "ELOB",
+    "UBA2",
+    "NDUFB10",
+    "TP53",
+    "EXOSC8",
+    "PRPF31",
+    "NOP10",
+    "METTL9",
+    "DGUOK",
+    "PRPF38B",
+    "RHOF",
+    "MLF2",
+    "ATP2A2",
+    "DCTD",
+    "CHD2",
+    "PSMD9",
+    "WAS",
+    "CTDSP1",
+    "TNIP2",
+    "NDUFB5",
+    "SMAD3",
+    "TPX2",
+    "NEMF",
+    "SMARCA4",
+    "KAT2B",
+    "AKT1",
+    "METTL26",
+    "BNIP2",
+    "IQGAP2",
+    "METTL5",
+    "SMARCB1",
+    "TOP2A",
+    "SELENOK",
+    "RNF167",
+    "IMPDH2",
+    "UBE4A",
+    "MAP4K1",
+    "FASN",
+    "AP1M1",
+    "GLUL",
+    "MAP2K2",
+    "CMC2",
+    "CASC3",
+    "STAG2",
+    "CGGBP1",
+    "CBX3",
+    "MLLT6",
+    "UBE2R2",
+    "IRF4",
+    "ATP5MG",
+    "HMGB2",
+    "ARPC4",
+    "MDM4",
+    "SUN2",
+    "MBD2",
+    "TMSB10",
+    "C11orf58",
+    "TMEM50A",
+    "SMS",
+    "TMEM33",
+    "SNU13",
+    "LGALS1",
+    "GTF2A2",
+    "VDAC3",
+    "S100A11",
+    "NME1",
+    "TUT7",
+    "AIMP1",
+    "ZC3HAV1",
+    "UFM1",
+    "SRSF2",
+    "CD40LG",
+    "CYTH1",
+    "S100A6",
+    "BAG6",
+    "ANAPC11",
+    "HECA",
+    "UCP2",
+    "OSTF1",
+    "SEPTIN1",
+    "PSMA2",
+    "CD28",
+    "ANXA2",
+    "CAPZA1",
+    "BRD2",
+    "ZNF644",
+    "CYBA",
+    "NUDT5"
+   ],
+   "control_symbols_missing": [
+    "GPN3",
+    "NCAPG",
+    "PRPF4",
+    "IMP3",
+    "ZMAT2",
+    "PNN",
+    "HGS",
+    "EBNA1BP2",
+    "TMSB4X",
+    "EIF3B",
+    "NCL",
+    "MT-ND3"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 138,
+   "control_ensembl": [
+    "ENSG00000100342",
+    "ENSG00000160796",
+    "ENSG00000146278",
+    "ENSG00000154727",
+    "ENSG00000114520",
+    "ENSG00000107929",
+    "ENSG00000171522",
+    "ENSG00000064419",
+    "ENSG00000160613",
+    "ENSG00000141452",
+    "ENSG00000100351",
+    "ENSG00000126254",
+    "ENSG00000168118",
+    "ENSG00000176783",
+    "ENSG00000102908",
+    "ENSG00000099624",
+    "ENSG00000170802",
+    "ENSG00000094916",
+    "ENSG00000064115",
+    "ENSG00000184508",
+    "ENSG00000076604",
+    "ENSG00000136731",
+    "ENSG00000123130",
+    "ENSG00000140379",
+    "ENSG00000122952",
+    "ENSG00000115946",
+    "ENSG00000146576",
+    "ENSG00000162654",
+    "ENSG00000139718",
+    "ENSG00000002834",
+    "ENSG00000099341",
+    "ENSG00000102103",
+    "ENSG00000103769",
+    "ENSG00000104325",
+    "ENSG00000143575",
+    "ENSG00000115286",
+    "ENSG00000177700",
+    "ENSG00000085224",
+    "ENSG00000135341",
+    "ENSG00000104231",
+    "ENSG00000131378",
+    "ENSG00000165060",
+    "ENSG00000135541",
+    "ENSG00000168883",
+    "ENSG00000105576",
+    "ENSG00000101150",
+    "ENSG00000134717",
+    "ENSG00000010292",
+    "ENSG00000141682",
+    "ENSG00000108106",
+    "ENSG00000103363",
+    "ENSG00000126261",
+    "ENSG00000140990",
+    "ENSG00000141510",
+    "ENSG00000120699",
+    "ENSG00000105618",
+    "ENSG00000182117",
+    "ENSG00000197006",
+    "ENSG00000114956",
+    "ENSG00000134186",
+    "ENSG00000139725",
+    "ENSG00000089693",
+    "ENSG00000174437",
+    "ENSG00000129187",
+    "ENSG00000173575",
+    "ENSG00000110801",
+    "ENSG00000015285",
+    "ENSG00000144579",
+    "ENSG00000168884",
+    "ENSG00000136521",
+    "ENSG00000166949",
+    "ENSG00000088325",
+    "ENSG00000165525",
+    "ENSG00000127616",
+    "ENSG00000114166",
+    "ENSG00000142208",
+    "ENSG00000130731",
+    "ENSG00000140299",
+    "ENSG00000145703",
+    "ENSG00000138382",
+    "ENSG00000099956",
+    "ENSG00000131747",
+    "ENSG00000113811",
+    "ENSG00000108523",
+    "ENSG00000178035",
+    "ENSG00000110344",
+    "ENSG00000104814",
+    "ENSG00000169710",
+    "ENSG00000072958",
+    "ENSG00000135821",
+    "ENSG00000126934",
+    "ENSG00000103121",
+    "ENSG00000108349",
+    "ENSG00000101972",
+    "ENSG00000163320",
+    "ENSG00000122565",
+    "ENSG00000275023",
+    "ENSG00000107341",
+    "ENSG00000137265",
+    "ENSG00000167283",
+    "ENSG00000164104",
+    "ENSG00000241553",
+    "ENSG00000198625",
+    "ENSG00000100242",
+    "ENSG00000134046",
+    "ENSG00000034510",
+    "ENSG00000110696",
+    "ENSG00000183726",
+    "ENSG00000102172",
+    "ENSG00000109133",
+    "ENSG00000100138",
+    "ENSG00000100097",
+    "ENSG00000140307",
+    "ENSG00000078668",
+    "ENSG00000163191",
+    "ENSG00000239672",
+    "ENSG00000083223",
+    "ENSG00000164022",
+    "ENSG00000105939",
+    "ENSG00000120686",
+    "ENSG00000161547",
+    "ENSG00000102245",
+    "ENSG00000108669",
+    "ENSG00000197956",
+    "ENSG00000204463",
+    "ENSG00000141552",
+    "ENSG00000112406",
+    "ENSG00000175567",
+    "ENSG00000134996",
+    "ENSG00000180096",
+    "ENSG00000106588",
+    "ENSG00000178562",
+    "ENSG00000182718",
+    "ENSG00000116489",
+    "ENSG00000204256",
+    "ENSG00000122482",
+    "ENSG00000051523",
+    "ENSG00000165609"
+   ]
+  },
+  {
+   "program_id": "th2_like",
+   "score_field": "th2_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.25,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 4,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "PTGDR2",
+    "IL4",
+    "IL5",
+    "IL13"
+   ],
+   "panel_symbols_retained": [
+    "PTGDR2",
+    "IL4",
+    "IL5",
+    "IL13"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 4,
+   "n_panel_in_effect_universe": 4,
+   "panel_ensembl": [
+    "ENSG00000183134",
+    "ENSG00000113520",
+    "ENSG00000113525",
+    "ENSG00000169194"
+   ],
+   "control_symbols_retained": [
+    "BEST4",
+    "RPH3AL",
+    "ASAP2",
+    "ETV7",
+    "PITX1",
+    "DENND2B",
+    "NCF1",
+    "SCN8A",
+    "NOS3",
+    "ZNF695",
+    "RNF217",
+    "GLDC",
+    "WWTR1",
+    "KRT18",
+    "PPM1N",
+    "NMU",
+    "PRKAR2B",
+    "RHBDL1",
+    "HNF1B",
+    "MC1R",
+    "COL5A2",
+    "SPTBN5",
+    "ADAMTSL5",
+    "CKB",
+    "TP53I3",
+    "CLK2",
+    "CKAP4",
+    "GCNA",
+    "SULT1B1",
+    "ERP27",
+    "SCN9A",
+    "ZNF699",
+    "DCBLD2",
+    "LIN7A",
+    "AK9",
+    "KIAA1191",
+    "RAB30",
+    "RNF122",
+    "ZSWIM3",
+    "RNF130",
+    "SANBR",
+    "CYB561",
+    "ID3",
+    "GM2A",
+    "IL22",
+    "WDR19",
+    "TMCC1",
+    "EPM2A",
+    "EPHX2",
+    "MBD5",
+    "FCER1G",
+    "ZNF17",
+    "FSD1",
+    "ZNF235",
+    "CHST10",
+    "FSD1L",
+    "ZKSCAN3",
+    "IFT122",
+    "ASB13",
+    "BPHL",
+    "CEACAM1",
+    "FCGRT",
+    "KIF27",
+    "ZNF821",
+    "VPS9D1",
+    "CPNE8",
+    "ZFP69B",
+    "PLEKHA1",
+    "ZNF585B",
+    "ZNF606",
+    "TRIO",
+    "TMEM126A",
+    "TMED7",
+    "TFAM",
+    "TAOK3",
+    "ACAA1",
+    "NPC2",
+    "SLC5A3",
+    "FOXO1",
+    "SNAPC3",
+    "PTAR1",
+    "AURKAIP1",
+    "TENT2",
+    "IRF9",
+    "AIMP2",
+    "SH3BP5",
+    "PRIM1",
+    "FUS",
+    "TNIK",
+    "PRRC2A",
+    "ICAM2",
+    "PURB",
+    "YTHDF3",
+    "FOXK2",
+    "CCDC12",
+    "N4BP2",
+    "MED8",
+    "AFG3L2",
+    "ATG5",
+    "CENPH",
+    "RIN3",
+    "YJU2",
+    "SEC14L1",
+    "NKTR",
+    "P2RY8",
+    "HK2",
+    "ZNF655",
+    "EHMT2",
+    "CPSF2",
+    "ARID2",
+    "CDKN1B",
+    "PAG1",
+    "MED30",
+    "ARID5A"
+   ],
+   "control_symbols_missing": [
+    "ADAMTS4",
+    "GAL",
+    "CILP2",
+    "CCER2",
+    "C2orf66",
+    "ITGA7",
+    "CCDC153",
+    "SRRM5",
+    "CAMK2N2",
+    "THNSL2",
+    "GPD1",
+    "NT5C1A",
+    "LIPH",
+    "LRG1",
+    "CRIP2",
+    "HBQ1",
+    "GREM2",
+    "NYAP1",
+    "DUSP29",
+    "NRSN2",
+    "DOC2A",
+    "PTPRF",
+    "TPBGL",
+    "GK3",
+    "DCAF4L1",
+    "EPHB4",
+    "HAL",
+    "LTO1",
+    "FAM114A1",
+    "TERF2",
+    "CEBPZOS",
+    "PLSCR3",
+    "SF3B1",
+    "IKBKG",
+    "OSBP",
+    "NUP155"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 114,
+   "control_ensembl": [
+    "ENSG00000142959",
+    "ENSG00000181031",
+    "ENSG00000151693",
+    "ENSG00000010030",
+    "ENSG00000069011",
+    "ENSG00000166444",
+    "ENSG00000158517",
+    "ENSG00000196876",
+    "ENSG00000164867",
+    "ENSG00000197472",
+    "ENSG00000146373",
+    "ENSG00000178445",
+    "ENSG00000018408",
+    "ENSG00000111057",
+    "ENSG00000213889",
+    "ENSG00000109255",
+    "ENSG00000005249",
+    "ENSG00000103269",
+    "ENSG00000275410",
+    "ENSG00000258839",
+    "ENSG00000204262",
+    "ENSG00000137877",
+    "ENSG00000185761",
+    "ENSG00000166165",
+    "ENSG00000115129",
+    "ENSG00000176444",
+    "ENSG00000136026",
+    "ENSG00000147174",
+    "ENSG00000173597",
+    "ENSG00000139055",
+    "ENSG00000169432",
+    "ENSG00000196110",
+    "ENSG00000057019",
+    "ENSG00000111052",
+    "ENSG00000155085",
+    "ENSG00000122203",
+    "ENSG00000137502",
+    "ENSG00000133874",
+    "ENSG00000132801",
+    "ENSG00000113269",
+    "ENSG00000162929",
+    "ENSG00000008283",
+    "ENSG00000117318",
+    "ENSG00000196743",
+    "ENSG00000127318",
+    "ENSG00000157796",
+    "ENSG00000172765",
+    "ENSG00000112425",
+    "ENSG00000120915",
+    "ENSG00000204406",
+    "ENSG00000158869",
+    "ENSG00000186272",
+    "ENSG00000105255",
+    "ENSG00000159917",
+    "ENSG00000115526",
+    "ENSG00000106701",
+    "ENSG00000189298",
+    "ENSG00000163913",
+    "ENSG00000196372",
+    "ENSG00000137274",
+    "ENSG00000079385",
+    "ENSG00000104870",
+    "ENSG00000165115",
+    "ENSG00000102984",
+    "ENSG00000075399",
+    "ENSG00000139117",
+    "ENSG00000187801",
+    "ENSG00000107679",
+    "ENSG00000245680",
+    "ENSG00000166704",
+    "ENSG00000038382",
+    "ENSG00000171202",
+    "ENSG00000134970",
+    "ENSG00000108064",
+    "ENSG00000135090",
+    "ENSG00000060971",
+    "ENSG00000119655",
+    "ENSG00000198743",
+    "ENSG00000150907",
+    "ENSG00000164975",
+    "ENSG00000188647",
+    "ENSG00000175756",
+    "ENSG00000164329",
+    "ENSG00000213928",
+    "ENSG00000106305",
+    "ENSG00000131370",
+    "ENSG00000198056",
+    "ENSG00000089280",
+    "ENSG00000154310",
+    "ENSG00000204469",
+    "ENSG00000108622",
+    "ENSG00000146676",
+    "ENSG00000185728",
+    "ENSG00000141568",
+    "ENSG00000160799",
+    "ENSG00000078177",
+    "ENSG00000159479",
+    "ENSG00000141385",
+    "ENSG00000057663",
+    "ENSG00000153044",
+    "ENSG00000100599",
+    "ENSG00000105248",
+    "ENSG00000129657",
+    "ENSG00000114857",
+    "ENSG00000182162",
+    "ENSG00000159399",
+    "ENSG00000197343",
+    "ENSG00000204371",
+    "ENSG00000165934",
+    "ENSG00000189079",
+    "ENSG00000111276",
+    "ENSG00000076641",
+    "ENSG00000164758",
+    "ENSG00000196843"
+   ]
+  },
+  {
+   "program_id": "th17_like",
+   "score_field": "th17_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.1666666667,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 6,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "CCR6",
+    "RORC",
+    "IL17A",
+    "IL17F",
+    "IL23R",
+    "KLRB1"
+   ],
+   "panel_symbols_retained": [
+    "CCR6",
+    "RORC",
+    "IL17F",
+    "IL23R",
+    "KLRB1"
+   ],
+   "panel_symbols_missing": [
+    "IL17A"
+   ],
+   "n_panel_symbols": 6,
+   "n_panel_in_effect_universe": 5,
+   "panel_ensembl": [
+    "ENSG00000112486",
+    "ENSG00000143365",
+    "ENSG00000112116",
+    "ENSG00000162594",
+    "ENSG00000111796"
+   ],
+   "control_symbols_retained": [
+    "GLI1",
+    "SLC22A23",
+    "DOK3",
+    "KLHL13",
+    "SV2C",
+    "F2RL1",
+    "RNF212",
+    "LZTS3",
+    "CELSR2",
+    "DYNLT4",
+    "ZNF730",
+    "PHACTR1",
+    "NCF1",
+    "ME1",
+    "GSDMA",
+    "WWTR1",
+    "CTSF",
+    "IL7",
+    "NLGN3",
+    "PROCR",
+    "NR6A1",
+    "EGFL7",
+    "SLC23A3",
+    "FCGBP",
+    "C11orf65",
+    "UNC5CL",
+    "QPCT",
+    "PCBP3",
+    "LDHC",
+    "FBXO36",
+    "ATP8A2",
+    "LYG1",
+    "CEND1",
+    "PRRG2",
+    "ZNF677",
+    "ZGLP1",
+    "HPGDS",
+    "MET",
+    "LOXL1",
+    "ZNF713",
+    "NCR3LG1",
+    "TMEM265",
+    "SLCO4C1",
+    "PIK3R6",
+    "ASS1",
+    "TSSK4",
+    "RBM11",
+    "CDO1",
+    "HS3ST1",
+    "OAZ3",
+    "LMTK3",
+    "ZDHHC23",
+    "DNAJB5",
+    "ZNF747",
+    "ZG16B",
+    "ZMAT1",
+    "ZNF852",
+    "CARNS1",
+    "PER3"
+   ],
+   "control_symbols_missing": [
+    "MEOX1",
+    "MDH1B",
+    "CDC42EP4",
+    "CRYBA4",
+    "SOX8",
+    "PXDC1",
+    "NKAPL",
+    "C12orf56",
+    "ECHDC3",
+    "CFAP92",
+    "JAKMIP3",
+    "ASB12",
+    "GPR176",
+    "DNAH14",
+    "IGHE",
+    "CFAP276",
+    "HSPA12A",
+    "SMAD9",
+    "ARMCX1",
+    "TAL2",
+    "OVOL1",
+    "ODAD3",
+    "COL11A2",
+    "LIN28A",
+    "SLC39A2",
+    "GFRA3",
+    "MSMP",
+    "NDUFA4L2",
+    "OPRL1",
+    "TRIM2",
+    "ADRA1B",
+    "ZNF660",
+    "GALNT14",
+    "LMAN1L",
+    "NEFL",
+    "LRGUK",
+    "DLGAP3",
+    "SCNN1A",
+    "PTN",
+    "TMSB15A",
+    "MAJIN",
+    "ZNF703",
+    "HK3",
+    "PAX5",
+    "CCER2",
+    "H2BK1",
+    "SLC34A1",
+    "DDX4",
+    "SRGAP3",
+    "GNG12",
+    "NGEF",
+    "DCAF4L1",
+    "TGM5",
+    "ULBP1",
+    "DEGS2",
+    "MEX3A",
+    "ASPHD1",
+    "FZD8",
+    "DOCK8-AS1",
+    "SSC4D",
+    "LRP1",
+    "UACA",
+    "RDH16",
+    "THSD1",
+    "FCER2",
+    "LINGO3",
+    "FAM151B",
+    "PPFIA3",
+    "LRRC66",
+    "TTLL13",
+    "TRIM9",
+    "TAGLN3",
+    "PAPSS2",
+    "ZNF404",
+    "OR2AG2",
+    "ADGRD1",
+    "LRRK1",
+    "TLR3",
+    "GALNT8",
+    "CCDC113",
+    "CCDC121",
+    "ATRNL1",
+    "SUSD4",
+    "SHB",
+    "CCDC157",
+    "KANK2",
+    "ADAMTS7",
+    "AMH",
+    "KDM4D",
+    "NINL",
+    "CCL20"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 59,
+   "control_ensembl": [
+    "ENSG00000111087",
+    "ENSG00000137266",
+    "ENSG00000146094",
+    "ENSG00000003096",
+    "ENSG00000122012",
+    "ENSG00000164251",
+    "ENSG00000178222",
+    "ENSG00000088899",
+    "ENSG00000143126",
+    "ENSG00000188396",
+    "ENSG00000183850",
+    "ENSG00000112137",
+    "ENSG00000158517",
+    "ENSG00000065833",
+    "ENSG00000167914",
+    "ENSG00000018408",
+    "ENSG00000174080",
+    "ENSG00000104432",
+    "ENSG00000196338",
+    "ENSG00000101000",
+    "ENSG00000148200",
+    "ENSG00000172889",
+    "ENSG00000213901",
+    "ENSG00000275395",
+    "ENSG00000166323",
+    "ENSG00000124602",
+    "ENSG00000115828",
+    "ENSG00000183570",
+    "ENSG00000166796",
+    "ENSG00000153832",
+    "ENSG00000132932",
+    "ENSG00000144214",
+    "ENSG00000184524",
+    "ENSG00000126460",
+    "ENSG00000197928",
+    "ENSG00000220201",
+    "ENSG00000163106",
+    "ENSG00000105976",
+    "ENSG00000129038",
+    "ENSG00000178665",
+    "ENSG00000188211",
+    "ENSG00000281991",
+    "ENSG00000173930",
+    "ENSG00000276231",
+    "ENSG00000130707",
+    "ENSG00000139908",
+    "ENSG00000185272",
+    "ENSG00000129596",
+    "ENSG00000002587",
+    "ENSG00000143450",
+    "ENSG00000142235",
+    "ENSG00000184307",
+    "ENSG00000137094",
+    "ENSG00000169955",
+    "ENSG00000162078",
+    "ENSG00000166432",
+    "ENSG00000178917",
+    "ENSG00000172508",
+    "ENSG00000049246"
+   ]
+  },
+  {
+   "program_id": "tfh_like",
+   "score_field": "tfh_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.3333333333,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 3,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "CXCR5",
+    "BCL6",
+    "IL21"
+   ],
+   "panel_symbols_retained": [
+    "CXCR5",
+    "BCL6",
+    "IL21"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 3,
+   "n_panel_in_effect_universe": 3,
+   "panel_ensembl": [
+    "ENSG00000160683",
+    "ENSG00000113916",
+    "ENSG00000138684"
+   ],
+   "control_symbols_retained": [
+    "ADGRL1",
+    "C20orf96",
+    "PWWP2B",
+    "C16orf86",
+    "SLC35A2",
+    "RNASE6",
+    "MDGA1",
+    "ODF3B",
+    "TPCN2",
+    "NPL",
+    "SLC16A10",
+    "TUBB2A",
+    "ARMCX2",
+    "ADM5",
+    "SLC25A53",
+    "PODXL2",
+    "TNFRSF10D",
+    "CYSLTR2",
+    "ZNF257",
+    "EML5",
+    "HSPA4L",
+    "TSSK6",
+    "KBTBD11",
+    "TSGA10",
+    "RAB15",
+    "FGFBP3",
+    "DYNLL1",
+    "MAFF",
+    "CTTNBP2NL",
+    "TCF4",
+    "ZNF823",
+    "FAAH2",
+    "SYP",
+    "ACTR3B",
+    "ZNF215",
+    "ZNF57",
+    "ACE",
+    "UQCC4",
+    "HYKK",
+    "ZNF879",
+    "SPRED2",
+    "NAP1L5",
+    "ZNF235",
+    "SLC22A5",
+    "SPINT2",
+    "TMEM229B",
+    "HSPA1L",
+    "C3AR1",
+    "IGFBP4",
+    "MSC",
+    "NAT14",
+    "CSGALNACT1",
+    "TMEM169",
+    "HIC2",
+    "H4C11",
+    "ZNF780B",
+    "ZNF585A",
+    "FIZ1",
+    "LMAN2L",
+    "SLC29A2",
+    "SESTD1",
+    "PRDM15",
+    "BTBD3",
+    "IL10",
+    "RAD52",
+    "DCBLD2",
+    "ZFY",
+    "EPAS1",
+    "IFNGR2",
+    "KLHL25",
+    "CEACAM1",
+    "NAALADL1",
+    "TTC7B",
+    "KRBOX4",
+    "FAM161A",
+    "DHRS1",
+    "USP35",
+    "TSPAN2",
+    "CBY1",
+    "AGRN",
+    "DPP3",
+    "ZNF16",
+    "JAZF1",
+    "REXO5",
+    "ZFP69B",
+    "IRAK1BP1",
+    "GHDC",
+    "CTTN",
+    "RIC3",
+    "B3GALNT2",
+    "KAT14",
+    "TBC1D24",
+    "EEF2KMT",
+    "SERPINE2",
+    "NAPB",
+    "CDADC1",
+    "ZNF792",
+    "RPUSD2",
+    "DPY19L4",
+    "OGFOD2",
+    "CPT1A",
+    "CYB5R1",
+    "EARS2",
+    "SCAI",
+    "DEXI",
+    "PER2",
+    "RHOU",
+    "TMEM241",
+    "NSUN5",
+    "NDRG1",
+    "CC2D1B",
+    "HSD17B12",
+    "C1RL",
+    "PIR",
+    "ABHD14A",
+    "DCAF4",
+    "FDXACB1",
+    "TMEM222",
+    "SEMA4C",
+    "ZNF574",
+    "DPM3",
+    "PTCD2",
+    "GCNT1",
+    "DHX34",
+    "UBXN8",
+    "ALKBH4",
+    "ZNF841",
+    "PEX14",
+    "BAD",
+    "KIFAP3",
+    "PBX3",
+    "GFOD2",
+    "IL4R",
+    "ARHGEF39"
+   ],
+   "control_symbols_missing": [
+    "CHTF8",
+    "ZNF683",
+    "ERMN",
+    "PIGZ",
+    "C12orf60",
+    "FSTL3",
+    "MISFA",
+    "C6orf52",
+    "KANTR",
+    "TANC2",
+    "UBFD1",
+    "SHLD3",
+    "GINS4",
+    "MT-ND2",
+    "ZNF207",
+    "POU2F1"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 134,
+   "control_ensembl": [
+    "ENSG00000072071",
+    "ENSG00000196476",
+    "ENSG00000171813",
+    "ENSG00000159761",
+    "ENSG00000102100",
+    "ENSG00000169413",
+    "ENSG00000112139",
+    "ENSG00000177989",
+    "ENSG00000162341",
+    "ENSG00000135838",
+    "ENSG00000112394",
+    "ENSG00000137267",
+    "ENSG00000184867",
+    "ENSG00000224420",
+    "ENSG00000269743",
+    "ENSG00000114631",
+    "ENSG00000173530",
+    "ENSG00000152207",
+    "ENSG00000197134",
+    "ENSG00000165521",
+    "ENSG00000164070",
+    "ENSG00000178093",
+    "ENSG00000176595",
+    "ENSG00000135951",
+    "ENSG00000139998",
+    "ENSG00000174721",
+    "ENSG00000088986",
+    "ENSG00000185022",
+    "ENSG00000143079",
+    "ENSG00000196628",
+    "ENSG00000197933",
+    "ENSG00000165591",
+    "ENSG00000102003",
+    "ENSG00000133627",
+    "ENSG00000149054",
+    "ENSG00000171970",
+    "ENSG00000159640",
+    "ENSG00000174109",
+    "ENSG00000188266",
+    "ENSG00000234284",
+    "ENSG00000198369",
+    "ENSG00000177432",
+    "ENSG00000159917",
+    "ENSG00000197375",
+    "ENSG00000167642",
+    "ENSG00000198133",
+    "ENSG00000204390",
+    "ENSG00000171860",
+    "ENSG00000141753",
+    "ENSG00000178860",
+    "ENSG00000090971",
+    "ENSG00000147408",
+    "ENSG00000163449",
+    "ENSG00000169635",
+    "ENSG00000197238",
+    "ENSG00000128000",
+    "ENSG00000196967",
+    "ENSG00000179943",
+    "ENSG00000114988",
+    "ENSG00000174669",
+    "ENSG00000187231",
+    "ENSG00000141956",
+    "ENSG00000132640",
+    "ENSG00000136634",
+    "ENSG00000002016",
+    "ENSG00000057019",
+    "ENSG00000067646",
+    "ENSG00000116016",
+    "ENSG00000159128",
+    "ENSG00000183655",
+    "ENSG00000079385",
+    "ENSG00000168060",
+    "ENSG00000165914",
+    "ENSG00000147121",
+    "ENSG00000170264",
+    "ENSG00000157379",
+    "ENSG00000118369",
+    "ENSG00000134198",
+    "ENSG00000100211",
+    "ENSG00000188157",
+    "ENSG00000254986",
+    "ENSG00000170631",
+    "ENSG00000153814",
+    "ENSG00000005189",
+    "ENSG00000187801",
+    "ENSG00000146243",
+    "ENSG00000167925",
+    "ENSG00000085733",
+    "ENSG00000166405",
+    "ENSG00000162885",
+    "ENSG00000149474",
+    "ENSG00000162065",
+    "ENSG00000118894",
+    "ENSG00000135919",
+    "ENSG00000125814",
+    "ENSG00000102543",
+    "ENSG00000180884",
+    "ENSG00000166133",
+    "ENSG00000156162",
+    "ENSG00000111325",
+    "ENSG00000110090",
+    "ENSG00000159348",
+    "ENSG00000103356",
+    "ENSG00000173611",
+    "ENSG00000182108",
+    "ENSG00000132326",
+    "ENSG00000116574",
+    "ENSG00000134490",
+    "ENSG00000130305",
+    "ENSG00000104419",
+    "ENSG00000154222",
+    "ENSG00000149084",
+    "ENSG00000139178",
+    "ENSG00000087842",
+    "ENSG00000248487",
+    "ENSG00000119599",
+    "ENSG00000255561",
+    "ENSG00000186501",
+    "ENSG00000168758",
+    "ENSG00000105732",
+    "ENSG00000179085",
+    "ENSG00000049883",
+    "ENSG00000187210",
+    "ENSG00000134815",
+    "ENSG00000104691",
+    "ENSG00000160993",
+    "ENSG00000197608",
+    "ENSG00000142655",
+    "ENSG00000002330",
+    "ENSG00000075945",
+    "ENSG00000167081",
+    "ENSG00000141098",
+    "ENSG00000077238",
+    "ENSG00000137135"
+   ]
+  },
+  {
+   "program_id": "treg_like",
+   "score_field": "treg_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.2,
+    "control_coef": -0.004,
+    "n_measured_panel": 5,
+    "n_control": 250
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "FOXP3",
+    "IKZF2",
+    "CTLA4",
+    "CCR8",
+    "TNFRSF18"
+   ],
+   "panel_symbols_retained": [
+    "FOXP3",
+    "IKZF2",
+    "CTLA4",
+    "CCR8",
+    "TNFRSF18"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 5,
+   "n_panel_in_effect_universe": 5,
+   "panel_ensembl": [
+    "ENSG00000049768",
+    "ENSG00000030419",
+    "ENSG00000163599",
+    "ENSG00000179934",
+    "ENSG00000186891"
+   ],
+   "control_symbols_retained": [
+    "THNSL1",
+    "RCN3",
+    "PANK1",
+    "OTOF",
+    "ZNF17",
+    "KIF9",
+    "TST",
+    "RAB30",
+    "ID3",
+    "NAGLU",
+    "PON2",
+    "MCF2L2",
+    "CDC42BPA",
+    "MAP4K3",
+    "ABAT",
+    "KRBOX4",
+    "NEK8",
+    "ARHGEF5",
+    "GCAT",
+    "CCDC141",
+    "ZNF296",
+    "ABL2",
+    "ITGB1BP2",
+    "ADCK5",
+    "ZNF628",
+    "PPARGC1B",
+    "ITGA1",
+    "TSPAN33",
+    "KCNQ1",
+    "ADRB2",
+    "SPRING1",
+    "ARMC9",
+    "CTPS2",
+    "IER5L",
+    "MBD5",
+    "ZNF496",
+    "ZKSCAN3",
+    "CPNE8",
+    "CRAT",
+    "KIAA1191",
+    "QPRT",
+    "H2BC3",
+    "SLC9A9",
+    "NLRX1",
+    "ZNF584",
+    "SH2D4A",
+    "CDKL1",
+    "CLCN5",
+    "ZBTB34",
+    "ATP6V0E2",
+    "ZNF8",
+    "DOK4",
+    "PDLIM7",
+    "IPO4",
+    "CITED4",
+    "LRRC37B",
+    "ARF3",
+    "SEMA4B",
+    "SPEF2",
+    "MAP1A",
+    "CYB5RL",
+    "ZNF568",
+    "DNAJC30",
+    "ACP6",
+    "ZNF740",
+    "SNX18",
+    "PTPN18",
+    "BBS10",
+    "FAM221A",
+    "INSL3",
+    "ZBTB18",
+    "C6orf47",
+    "IFT88",
+    "TOGARAM1",
+    "ZNF510",
+    "GOLM1",
+    "H6PD",
+    "PKD1",
+    "CBX1",
+    "ZNF714",
+    "RGL2",
+    "CASZ1",
+    "ABHD8",
+    "ENGASE",
+    "PRICKLE3",
+    "STK3",
+    "RBM43",
+    "NEFH",
+    "IRF5",
+    "DST",
+    "KAT2A",
+    "NEIL2",
+    "VPS16",
+    "ZNF808",
+    "HMGXB3",
+    "PRMT9",
+    "SLC25A23",
+    "ADAM9",
+    "KLHL28",
+    "CEP76",
+    "TKFC",
+    "GALC",
+    "WDR73",
+    "GBP3",
+    "ANGEL1",
+    "PCYT2",
+    "CRY2",
+    "DCAKD",
+    "CES2",
+    "HIKESHI",
+    "ERMARD",
+    "ZBTB39",
+    "SPPL3",
+    "TMEM164",
+    "ANKRD26",
+    "FAM50B",
+    "ATG16L1",
+    "TAPT1",
+    "DYNC2LI1",
+    "IFT46",
+    "ERLIN2",
+    "ATPSCKMT",
+    "GMCL1",
+    "MRI1",
+    "MPC1",
+    "ZFYVE27",
+    "STYXL1",
+    "LRWD1",
+    "CBR4",
+    "TRMT13",
+    "UVRAG",
+    "MUL1",
+    "CGRRF1",
+    "ING5",
+    "TMEM260",
+    "HCFC2",
+    "KLF11",
+    "ACY1",
+    "CD99L2",
+    "MAN2B2",
+    "KCNN4",
+    "PDE4B",
+    "PSAP",
+    "MTERF4",
+    "RNF31",
+    "COMMD2",
+    "DNAJA4",
+    "REXO4",
+    "HERC4",
+    "TEX261",
+    "RDX",
+    "CAPG",
+    "KIF1C",
+    "CEMIP2",
+    "YIF1A",
+    "TPGS1",
+    "PRPSAP2",
+    "TTL",
+    "SLC5A6",
+    "TRAF2",
+    "BAHD1",
+    "FEM1B",
+    "FAM241A",
+    "WDR54",
+    "PEX26",
+    "IL3",
+    "ORC1",
+    "COPS8",
+    "FCMR",
+    "HMG20B",
+    "MAGED2",
+    "CBX4",
+    "MED12",
+    "HEATR5B",
+    "EPC1",
+    "BAP1",
+    "GPCPD1",
+    "STAM",
+    "SLC30A7",
+    "DTL",
+    "NUMB",
+    "ANKRD40",
+    "TADA2B",
+    "CLIP4",
+    "ATN1",
+    "SEC61G",
+    "POU2AF1",
+    "PRR14",
+    "TADA3",
+    "RC3H1",
+    "TTC14",
+    "CD80",
+    "RAB11A",
+    "GOLGA3",
+    "FRYL",
+    "MBTPS1",
+    "B3GNT2",
+    "SNW1",
+    "GNA15",
+    "NONO",
+    "N4BP2",
+    "C18orf25",
+    "LASP1",
+    "CFAP97",
+    "NDC1",
+    "FOXK2",
+    "ITSN2",
+    "ISG20",
+    "TOR1AIP1",
+    "CDKAL1",
+    "MED6",
+    "FOXO1",
+    "TNPO3",
+    "AP1G2",
+    "ZNF217",
+    "UBE2N",
+    "PITPNB",
+    "PCYT1A",
+    "ZNF148",
+    "ZWINT",
+    "THUMPD3",
+    "EPB41",
+    "LSM10",
+    "IRF9",
+    "PSMD2",
+    "YJU2",
+    "ARL8A",
+    "IGFLR1",
+    "NUSAP1",
+    "MB21D2",
+    "MEPCE"
+   ],
+   "control_symbols_missing": [
+    "AKR1C8",
+    "PLA2G4B",
+    "VPS18",
+    "GPATCH1",
+    "KIAA1958",
+    "CDAN1",
+    "PPIL2",
+    "NUFIP1",
+    "UTP15",
+    "MED9",
+    "DHX33",
+    "GAK",
+    "VPS37A",
+    "CCT3",
+    "XRCC5",
+    "IK",
+    "WDR3",
+    "NUP155",
+    "GMPS"
+   ],
+   "n_control_symbols": 250,
+   "n_control_in_effect_universe": 231,
+   "control_ensembl": [
+    "ENSG00000185875",
+    "ENSG00000142552",
+    "ENSG00000152782",
+    "ENSG00000115155",
+    "ENSG00000186272",
+    "ENSG00000088727",
+    "ENSG00000128311",
+    "ENSG00000137502",
+    "ENSG00000117318",
+    "ENSG00000108784",
+    "ENSG00000105854",
+    "ENSG00000053524",
+    "ENSG00000143776",
+    "ENSG00000011566",
+    "ENSG00000183044",
+    "ENSG00000147121",
+    "ENSG00000160602",
+    "ENSG00000050327",
+    "ENSG00000100116",
+    "ENSG00000163492",
+    "ENSG00000170684",
+    "ENSG00000143322",
+    "ENSG00000147166",
+    "ENSG00000173137",
+    "ENSG00000197483",
+    "ENSG00000155846",
+    "ENSG00000213949",
+    "ENSG00000158457",
+    "ENSG00000053918",
+    "ENSG00000169252",
+    "ENSG00000111412",
+    "ENSG00000135931",
+    "ENSG00000047230",
+    "ENSG00000188483",
+    "ENSG00000204406",
+    "ENSG00000162714",
+    "ENSG00000189298",
+    "ENSG00000139117",
+    "ENSG00000095321",
+    "ENSG00000122203",
+    "ENSG00000103485",
+    "ENSG00000276410",
+    "ENSG00000181804",
+    "ENSG00000160703",
+    "ENSG00000171574",
+    "ENSG00000104611",
+    "ENSG00000100490",
+    "ENSG00000171365",
+    "ENSG00000177125",
+    "ENSG00000171130",
+    "ENSG00000278129",
+    "ENSG00000125170",
+    "ENSG00000196923",
+    "ENSG00000196497",
+    "ENSG00000179862",
+    "ENSG00000185158",
+    "ENSG00000134287",
+    "ENSG00000185033",
+    "ENSG00000152582",
+    "ENSG00000166963",
+    "ENSG00000215883",
+    "ENSG00000198453",
+    "ENSG00000176410",
+    "ENSG00000162836",
+    "ENSG00000139651",
+    "ENSG00000178996",
+    "ENSG00000072135",
+    "ENSG00000179941",
+    "ENSG00000188732",
+    "ENSG00000248099",
+    "ENSG00000179456",
+    "ENSG00000204439",
+    "ENSG00000032742",
+    "ENSG00000198718",
+    "ENSG00000081386",
+    "ENSG00000135052",
+    "ENSG00000049239",
+    "ENSG00000008710",
+    "ENSG00000108468",
+    "ENSG00000160352",
+    "ENSG00000237441",
+    "ENSG00000130940",
+    "ENSG00000127220",
+    "ENSG00000167280",
+    "ENSG00000012211",
+    "ENSG00000104375",
+    "ENSG00000184898",
+    "ENSG00000100285",
+    "ENSG00000128604",
+    "ENSG00000151914",
+    "ENSG00000108773",
+    "ENSG00000154328",
+    "ENSG00000215305",
+    "ENSG00000198482",
+    "ENSG00000113716",
+    "ENSG00000164169",
+    "ENSG00000125648",
+    "ENSG00000168615",
+    "ENSG00000179454",
+    "ENSG00000101624",
+    "ENSG00000149476",
+    "ENSG00000054983",
+    "ENSG00000177082",
+    "ENSG00000117226",
+    "ENSG00000013523",
+    "ENSG00000185813",
+    "ENSG00000121671",
+    "ENSG00000172992",
+    "ENSG00000172831",
+    "ENSG00000149196",
+    "ENSG00000130023",
+    "ENSG00000166860",
+    "ENSG00000157837",
+    "ENSG00000157600",
+    "ENSG00000107890",
+    "ENSG00000145945",
+    "ENSG00000085978",
+    "ENSG00000169762",
+    "ENSG00000138036",
+    "ENSG00000118096",
+    "ENSG00000147475",
+    "ENSG00000150756",
+    "ENSG00000087338",
+    "ENSG00000037757",
+    "ENSG00000060762",
+    "ENSG00000155256",
+    "ENSG00000127952",
+    "ENSG00000161036",
+    "ENSG00000145439",
+    "ENSG00000122435",
+    "ENSG00000198382",
+    "ENSG00000090432",
+    "ENSG00000100532",
+    "ENSG00000168395",
+    "ENSG00000070269",
+    "ENSG00000111727",
+    "ENSG00000172059",
+    "ENSG00000243989",
+    "ENSG00000102181",
+    "ENSG00000013288",
+    "ENSG00000104783",
+    "ENSG00000184588",
+    "ENSG00000197746",
+    "ENSG00000122085",
+    "ENSG00000092098",
+    "ENSG00000114744",
+    "ENSG00000140403",
+    "ENSG00000148300",
+    "ENSG00000148634",
+    "ENSG00000144043",
+    "ENSG00000137710",
+    "ENSG00000042493",
+    "ENSG00000129250",
+    "ENSG00000135048",
+    "ENSG00000174851",
+    "ENSG00000141933",
+    "ENSG00000141127",
+    "ENSG00000114999",
+    "ENSG00000138074",
+    "ENSG00000127191",
+    "ENSG00000140320",
+    "ENSG00000169018",
+    "ENSG00000174749",
+    "ENSG00000005448",
+    "ENSG00000215193",
+    "ENSG00000164399",
+    "ENSG00000085840",
+    "ENSG00000198612",
+    "ENSG00000162894",
+    "ENSG00000064961",
+    "ENSG00000102316",
+    "ENSG00000141582",
+    "ENSG00000184634",
+    "ENSG00000008869",
+    "ENSG00000120616",
+    "ENSG00000163930",
+    "ENSG00000125772",
+    "ENSG00000136738",
+    "ENSG00000162695",
+    "ENSG00000143476",
+    "ENSG00000133961",
+    "ENSG00000154945",
+    "ENSG00000173011",
+    "ENSG00000115295",
+    "ENSG00000111676",
+    "ENSG00000132432",
+    "ENSG00000110777",
+    "ENSG00000156858",
+    "ENSG00000171148",
+    "ENSG00000135870",
+    "ENSG00000163728",
+    "ENSG00000121594",
+    "ENSG00000103769",
+    "ENSG00000090615",
+    "ENSG00000075539",
+    "ENSG00000140943",
+    "ENSG00000170340",
+    "ENSG00000100603",
+    "ENSG00000060558",
+    "ENSG00000147140",
+    "ENSG00000078177",
+    "ENSG00000152242",
+    "ENSG00000002834",
+    "ENSG00000164323",
+    "ENSG00000058804",
+    "ENSG00000141568",
+    "ENSG00000198399",
+    "ENSG00000172183",
+    "ENSG00000143337",
+    "ENSG00000145996",
+    "ENSG00000133997",
+    "ENSG00000150907",
+    "ENSG00000064419",
+    "ENSG00000213983",
+    "ENSG00000171940",
+    "ENSG00000177889",
+    "ENSG00000180957",
+    "ENSG00000161217",
+    "ENSG00000163848",
+    "ENSG00000122952",
+    "ENSG00000134077",
+    "ENSG00000159023",
+    "ENSG00000181817",
+    "ENSG00000213928",
+    "ENSG00000175166",
+    "ENSG00000105248",
+    "ENSG00000143862",
+    "ENSG00000126246",
+    "ENSG00000137804",
+    "ENSG00000180611",
+    "ENSG00000146834"
+   ]
+  },
+  {
+   "program_id": "cd4_ctl_like",
+   "score_field": "cd4_ctl_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.1666666667,
+    "control_coef": -0.004,
+    "n_measured_panel": 6,
+    "n_control": 250
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "GNLY",
+    "PRF1",
+    "GZMH",
+    "KLRD1",
+    "GZMB",
+    "NKG7"
+   ],
+   "panel_symbols_retained": [
+    "GNLY",
+    "PRF1",
+    "GZMH",
+    "KLRD1",
+    "GZMB",
+    "NKG7"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 6,
+   "n_panel_in_effect_universe": 6,
+   "panel_ensembl": [
+    "ENSG00000115523",
+    "ENSG00000180644",
+    "ENSG00000100450",
+    "ENSG00000134539",
+    "ENSG00000100453",
+    "ENSG00000105374"
+   ],
+   "control_symbols_retained": [
+    "RBSN",
+    "LTBR",
+    "MXRA8",
+    "PPM1N",
+    "TUBB3",
+    "LBX2",
+    "ADAMTSL5",
+    "EFNB2",
+    "ZBTB47",
+    "COL18A1",
+    "IL12A",
+    "RAB3D",
+    "PLB1",
+    "NASP",
+    "GRHL1",
+    "TLR2",
+    "ZNF540",
+    "PITX1",
+    "NMU",
+    "ZNF555",
+    "FAM167B",
+    "SLC25A34",
+    "XKR9",
+    "ZNF572",
+    "NIPAL2",
+    "ZNF383",
+    "BEND5",
+    "SGPP2",
+    "TLK2",
+    "PHEX",
+    "RPP25",
+    "IPCEF1",
+    "PPP1R3F",
+    "ALG14",
+    "KAT2A",
+    "PLXNA4",
+    "SH2D3A",
+    "SMAD5",
+    "ZNF445",
+    "ST20",
+    "VILL",
+    "HMGN5",
+    "EVA1B",
+    "B4GAT1",
+    "ZNF133",
+    "KPTN",
+    "KBTBD3",
+    "NT5M",
+    "SLC30A4",
+    "TMEM203",
+    "BLVRB",
+    "RYK",
+    "LIN52",
+    "RAC3",
+    "TAF6L",
+    "TEDC2",
+    "SLC25A13",
+    "PHOSPHO2",
+    "PHC1",
+    "FARS2",
+    "PPARG",
+    "GRAMD2B",
+    "ATP5PF",
+    "DIXDC1",
+    "COQ8B",
+    "GPAM",
+    "SEMA4B",
+    "GSTA4",
+    "RGS2",
+    "DHRS7B",
+    "ZNF211",
+    "DXO",
+    "MSS51",
+    "ALKBH3",
+    "RPN2",
+    "HMBOX1",
+    "PDSS2",
+    "PAAF1",
+    "GATD1",
+    "SHMT1",
+    "MAFG",
+    "UBE2H",
+    "EXT1",
+    "PRUNE1",
+    "ST3GAL3",
+    "ARSA",
+    "DCAF6",
+    "ZMYM5",
+    "GRPEL2",
+    "SMYD5",
+    "BRF2",
+    "C19orf47",
+    "PHKG2",
+    "THAP7",
+    "BBX",
+    "CMC1",
+    "PSME3IP1",
+    "MTMR10",
+    "CAMK2G",
+    "KIAA0586",
+    "ALKBH7",
+    "FAM199X",
+    "LGALS3BP",
+    "SCYL3",
+    "METTL14",
+    "EID2",
+    "NEK6",
+    "JMJD4",
+    "TXK",
+    "TOP3B",
+    "GLIPR1",
+    "PCMTD2",
+    "CDYL",
+    "KIAA0408",
+    "ARID4A",
+    "ZNF263",
+    "MTAP",
+    "TBCEL",
+    "NCAPD2",
+    "RUNX3",
+    "VPS26A",
+    "NFE2L2",
+    "DEGS1",
+    "APEX1",
+    "STIM1",
+    "DAXX",
+    "CCNC",
+    "NCOA3",
+    "DNTTIP2",
+    "NCOA4",
+    "EHBP1L1",
+    "CHD4",
+    "PPP1R12A",
+    "EXOSC8",
+    "HPRT1",
+    "PPP2R2A",
+    "CHMP5",
+    "TMA7",
+    "PHF10",
+    "SRSF4",
+    "RUVBL1",
+    "STX16",
+    "OGT",
+    "TGFBR1",
+    "ADAM10",
+    "HSF1",
+    "PDE7A",
+    "BBLN",
+    "DNMT1",
+    "TOB1",
+    "RTN3",
+    "PCM1",
+    "NSA2",
+    "BCL3",
+    "ARHGAP25",
+    "ANAPC5",
+    "ENOPH1",
+    "ZFP36L2",
+    "SH3BP1",
+    "PCMT1",
+    "PUF60",
+    "PRPF31",
+    "NUMA1",
+    "EDF1",
+    "RCSD1",
+    "PAK2",
+    "CD3D",
+    "CD7",
+    "CYBA",
+    "COX16",
+    "SPTAN1",
+    "USF2",
+    "HECA",
+    "CDC42SE2",
+    "SDF4",
+    "EFHD2",
+    "SLC39A8",
+    "TMEM106C",
+    "DGKA",
+    "NOP53",
+    "HNRNPH3",
+    "LCK",
+    "IER5",
+    "RASSF5",
+    "CLDND1",
+    "LCP1",
+    "UCP2",
+    "LRRN3",
+    "SOCS1",
+    "EIF4A2",
+    "SNRPB2",
+    "RPA1",
+    "GNB2",
+    "SF3B3",
+    "NFKB2",
+    "ATP5PB",
+    "TOP1",
+    "CERS2",
+    "SEC11C",
+    "HAPSTR1",
+    "FAM32A",
+    "FIS1",
+    "LYAR",
+    "TNFRSF1B",
+    "ARF6",
+    "EZR",
+    "CREM",
+    "MAP7D1",
+    "ELL2",
+    "ARHGAP15",
+    "CD5",
+    "MYDGF"
+   ],
+   "control_symbols_missing": [
+    "SPON1",
+    "CES3",
+    "C16orf74",
+    "GK3",
+    "DOC2A",
+    "ZACN",
+    "ADAMTS14",
+    "OSCP1",
+    "ACOT12",
+    "GAL",
+    "OGDHL",
+    "CCDC62",
+    "TMEM54",
+    "SLC22A18AS",
+    "TTC16",
+    "CALHM1",
+    "NALF2",
+    "TMEM232",
+    "ERFE",
+    "UST",
+    "HDC",
+    "MYO1A",
+    "WNT7A",
+    "KIAA1522",
+    "SLC34A1",
+    "ENSG00000284691",
+    "BCLAF3",
+    "CCDC174",
+    "INTS1",
+    "ANAPC2",
+    "NAA50",
+    "CCDC86",
+    "PNISR",
+    "SMG5",
+    "RFLNB",
+    "ANKHD1",
+    "MAT2A",
+    "JAK3"
+   ],
+   "n_control_symbols": 250,
+   "n_control_in_effect_universe": 212,
+   "control_ensembl": [
+    "ENSG00000131381",
+    "ENSG00000111321",
+    "ENSG00000162576",
+    "ENSG00000213889",
+    "ENSG00000258947",
+    "ENSG00000179528",
+    "ENSG00000185761",
+    "ENSG00000125266",
+    "ENSG00000114853",
+    "ENSG00000182871",
+    "ENSG00000168811",
+    "ENSG00000105514",
+    "ENSG00000163803",
+    "ENSG00000132780",
+    "ENSG00000134317",
+    "ENSG00000137462",
+    "ENSG00000171817",
+    "ENSG00000069011",
+    "ENSG00000109255",
+    "ENSG00000186300",
+    "ENSG00000183615",
+    "ENSG00000162461",
+    "ENSG00000221947",
+    "ENSG00000180938",
+    "ENSG00000104361",
+    "ENSG00000188283",
+    "ENSG00000162373",
+    "ENSG00000163082",
+    "ENSG00000146872",
+    "ENSG00000102174",
+    "ENSG00000178718",
+    "ENSG00000074706",
+    "ENSG00000049769",
+    "ENSG00000172339",
+    "ENSG00000108773",
+    "ENSG00000221866",
+    "ENSG00000125731",
+    "ENSG00000113658",
+    "ENSG00000185219",
+    "ENSG00000180953",
+    "ENSG00000136059",
+    "ENSG00000198157",
+    "ENSG00000142694",
+    "ENSG00000174684",
+    "ENSG00000125846",
+    "ENSG00000118162",
+    "ENSG00000182359",
+    "ENSG00000205309",
+    "ENSG00000104154",
+    "ENSG00000187713",
+    "ENSG00000090013",
+    "ENSG00000163785",
+    "ENSG00000205659",
+    "ENSG00000169750",
+    "ENSG00000162227",
+    "ENSG00000162062",
+    "ENSG00000004864",
+    "ENSG00000144362",
+    "ENSG00000111752",
+    "ENSG00000145982",
+    "ENSG00000132170",
+    "ENSG00000155324",
+    "ENSG00000154723",
+    "ENSG00000150764",
+    "ENSG00000123815",
+    "ENSG00000119927",
+    "ENSG00000185033",
+    "ENSG00000170899",
+    "ENSG00000116741",
+    "ENSG00000109016",
+    "ENSG00000121417",
+    "ENSG00000204348",
+    "ENSG00000166343",
+    "ENSG00000166199",
+    "ENSG00000118705",
+    "ENSG00000147421",
+    "ENSG00000164494",
+    "ENSG00000175575",
+    "ENSG00000177225",
+    "ENSG00000176974",
+    "ENSG00000197063",
+    "ENSG00000186591",
+    "ENSG00000182197",
+    "ENSG00000143363",
+    "ENSG00000126091",
+    "ENSG00000100299",
+    "ENSG00000143164",
+    "ENSG00000132950",
+    "ENSG00000164284",
+    "ENSG00000135632",
+    "ENSG00000104221",
+    "ENSG00000160392",
+    "ENSG00000156873",
+    "ENSG00000184436",
+    "ENSG00000114439",
+    "ENSG00000187118",
+    "ENSG00000172775",
+    "ENSG00000166912",
+    "ENSG00000148660",
+    "ENSG00000100578",
+    "ENSG00000125652",
+    "ENSG00000123575",
+    "ENSG00000108679",
+    "ENSG00000000457",
+    "ENSG00000145388",
+    "ENSG00000176396",
+    "ENSG00000119408",
+    "ENSG00000081692",
+    "ENSG00000074966",
+    "ENSG00000100038",
+    "ENSG00000139278",
+    "ENSG00000203880",
+    "ENSG00000153046",
+    "ENSG00000189367",
+    "ENSG00000032219",
+    "ENSG00000006194",
+    "ENSG00000099810",
+    "ENSG00000154114",
+    "ENSG00000010292",
+    "ENSG00000020633",
+    "ENSG00000122958",
+    "ENSG00000116044",
+    "ENSG00000143753",
+    "ENSG00000100823",
+    "ENSG00000167323",
+    "ENSG00000204209",
+    "ENSG00000112237",
+    "ENSG00000124151",
+    "ENSG00000067334",
+    "ENSG00000266412",
+    "ENSG00000173442",
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+    "ENSG00000134291",
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+    "ENSG00000096746",
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+    "ENSG00000136167",
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+    "ENSG00000173114",
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+    "ENSG00000028137",
+    "ENSG00000165527",
+    "ENSG00000092820",
+    "ENSG00000095794",
+    "ENSG00000116871",
+    "ENSG00000118985",
+    "ENSG00000075884",
+    "ENSG00000110448",
+    "ENSG00000074842"
+   ]
+  },
+  {
+   "program_id": "th9_like",
+   "score_field": "th9_like_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": false,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
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+    "control_coef": -0.01,
+    "n_measured_panel": 2,
+    "n_control": 100
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "IL9",
+    "SPI1"
+   ],
+   "panel_symbols_retained": [],
+   "panel_symbols_missing": [
+    "IL9",
+    "SPI1"
+   ],
+   "n_panel_symbols": 2,
+   "n_panel_in_effect_universe": 0,
+   "panel_ensembl": [],
+   "control_symbols_retained": [
+    "TRGJP1",
+    "CLIC6",
+    "SCNN1D",
+    "PTAFR",
+    "TDRD9",
+    "BEST4",
+    "OR7D2",
+    "SALL2",
+    "AKAP12",
+    "OVGP1",
+    "MT1G",
+    "KLKB1",
+    "MSANTD1",
+    "XKR9",
+    "TIGD1",
+    "SMPDL3A",
+    "ANKRD50",
+    "PYROXD2",
+    "PXDN",
+    "ZNF730"
+   ],
+   "control_symbols_missing": [
+    "IFNK",
+    "GOLGA8R",
+    "ASCL1",
+    "STRC",
+    "FGF12",
+    "ABCA6",
+    "FBXO47",
+    "WEE2",
+    "ARHGAP20",
+    "IGDCC4",
+    "CGA",
+    "RARRES1",
+    "PAX9",
+    "UNC5A",
+    "HMGA2",
+    "KIAA0319",
+    "SH2D6",
+    "ARHGEF17",
+    "LCN6",
+    "MPC1L",
+    "TMEM132E",
+    "TEKT5",
+    "CCDC70",
+    "FGD5",
+    "KREMEN2",
+    "MRC1",
+    "RSPH6A",
+    "B3GNT7",
+    "AHNAK2",
+    "ZP1",
+    "ADRA2C",
+    "PDE6H",
+    "IL36RN",
+    "SMIM6",
+    "GALNT13",
+    "SLC7A9",
+    "M1AP",
+    "CBARP",
+    "CPLX4",
+    "CLGN",
+    "IQANK1",
+    "TAS2R50",
+    "CASR",
+    "RNF150",
+    "P2RY13",
+    "AP3B2",
+    "RNF224",
+    "CFAP99",
+    "KPNA7",
+    "TPH2",
+    "GHRL",
+    "TMEM269",
+    "CLTRN",
+    "REM2",
+    "PSPN",
+    "GML",
+    "ZACN",
+    "OR2AG2",
+    "ZNF404",
+    "KHDRBS3",
+    "CCDC168",
+    "UPK1A",
+    "SOX5",
+    "DENND2C",
+    "ALS2CL",
+    "NANOS3",
+    "RRH",
+    "ARHGEF33",
+    "PLA2G2C",
+    "RSKR",
+    "EPHB4",
+    "LRRK1",
+    "ADPRHL1",
+    "C16orf74",
+    "CPXM1",
+    "LEKR1",
+    "CELF6",
+    "TMEM232",
+    "CD1C",
+    "SNORC"
+   ],
+   "n_control_symbols": 100,
+   "n_control_in_effect_universe": 20,
+   "control_ensembl": [
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+    "ENSG00000159212",
+    "ENSG00000162572",
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+    "ENSG00000156414",
+    "ENSG00000142959",
+    "ENSG00000188000",
+    "ENSG00000165821",
+    "ENSG00000131016",
+    "ENSG00000085465",
+    "ENSG00000125144",
+    "ENSG00000164344",
+    "ENSG00000188981",
+    "ENSG00000221947",
+    "ENSG00000221944",
+    "ENSG00000172594",
+    "ENSG00000151458",
+    "ENSG00000119943",
+    "ENSG00000130508",
+    "ENSG00000183850"
+   ]
+  },
+  {
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+   "score_field": "diff_naive_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
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+    "control_coef": -0.005,
+    "n_measured_panel": 6,
+    "n_control": 200
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
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+    "SELL",
+    "TCF7",
+    "LEF1",
+    "IL7R",
+    "MAL"
+   ],
+   "panel_symbols_retained": [
+    "CCR7",
+    "SELL",
+    "TCF7",
+    "LEF1",
+    "IL7R",
+    "MAL"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 6,
+   "n_panel_in_effect_universe": 6,
+   "panel_ensembl": [
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+    "ENSG00000188404",
+    "ENSG00000081059",
+    "ENSG00000138795",
+    "ENSG00000168685",
+    "ENSG00000172005"
+   ],
+   "control_symbols_retained": [
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+    "FKBP8",
+    "ASPHD2",
+    "NPRL3",
+    "UBXN2A",
+    "ARL3",
+    "BLTP1",
+    "TSHZ2",
+    "KIF18B",
+    "LTBP3",
+    "UBE2H",
+    "GALK1",
+    "ZSWIM7",
+    "TRIM4",
+    "CC2D1A",
+    "ERCC2",
+    "HEG1",
+    "ZC3HC1",
+    "NUP35",
+    "SLC23A2",
+    "ATG9A",
+    "ATP7A",
+    "SCYL3",
+    "PLP2",
+    "DHX58",
+    "FAM199X",
+    "BRF2",
+    "MACO1",
+    "CIR1",
+    "RABIF",
+    "TAF5L",
+    "CWC25",
+    "YTHDF1",
+    "ILVBL",
+    "NDUFAF6",
+    "PWWP2A",
+    "TMEM120A",
+    "SH2B1",
+    "ORC5",
+    "TUBGCP5",
+    "HOMER2",
+    "RNF185",
+    "ELF2",
+    "FOXJ2",
+    "DENND1A",
+    "CLN8",
+    "FBXL4",
+    "EZH1",
+    "SLC11A2",
+    "VRK2",
+    "NF1",
+    "NR2C2AP",
+    "LSM3",
+    "THG1L",
+    "NMT2",
+    "EFL1",
+    "ZCCHC8",
+    "MRS2",
+    "RNASET2",
+    "PDPR",
+    "ZNF12",
+    "ITPR3",
+    "RXRB",
+    "CBR3",
+    "ESRRA",
+    "MAP3K13",
+    "C11orf24",
+    "EIF1AY",
+    "KHDC4",
+    "GAB2",
+    "MTFR2",
+    "MTMR3",
+    "ZDHHC14",
+    "TP53BP1",
+    "TSPAN3",
+    "C12orf29",
+    "PABPC1L",
+    "KCTD17",
+    "MSH3",
+    "NOP9",
+    "ABI2",
+    "MOSPD2",
+    "SPNS1",
+    "ZNF581",
+    "NUDT22",
+    "SMIM20",
+    "HPS4",
+    "TAF4",
+    "HAUS3",
+    "CCDC137",
+    "ABCB8",
+    "LFNG",
+    "NDUFS8",
+    "GTPBP10",
+    "ANKRD13B",
+    "ERH",
+    "TUBB",
+    "USO1",
+    "MAPRE1",
+    "CCNK",
+    "CIAO2A",
+    "MSH6",
+    "MIB1",
+    "ZDHHC20",
+    "VPS4B",
+    "FGFR1OP2",
+    "RALY",
+    "ANAPC15",
+    "GTPBP1",
+    "TNFRSF25",
+    "NOL7",
+    "ACTN4",
+    "PPID",
+    "AKAP13",
+    "PARL",
+    "DCUN1D1",
+    "MAML1",
+    "SCYL1",
+    "PRKACA",
+    "MLLT3",
+    "SMC2",
+    "TMED4",
+    "GSR",
+    "FLT3LG",
+    "THUMPD1",
+    "CLEC2B",
+    "RARA",
+    "BABAM1",
+    "PTEN",
+    "SP100",
+    "UBLCP1",
+    "IQGAP1",
+    "TRA2B",
+    "RPP30",
+    "GATAD2A",
+    "MPRIP",
+    "INTS6",
+    "UBE2F",
+    "EDC4",
+    "MCMBP",
+    "MANF",
+    "APBB1IP",
+    "MLLT6",
+    "GTF3A",
+    "STT3B",
+    "UFM1",
+    "SRSF2",
+    "MTHFD1",
+    "GNG2",
+    "ITM2A",
+    "MYDGF",
+    "OAS2",
+    "STK24",
+    "NDFIP2",
+    "THOC7",
+    "TOMM5",
+    "COX7A2",
+    "NDUFV1",
+    "SMC1A",
+    "HSP90AB1",
+    "CTSC",
+    "HSPA8",
+    "LITAF",
+    "GOLPH3",
+    "ACTR2",
+    "TCP1",
+    "CNBP",
+    "SPG21",
+    "MCM4",
+    "BIRC3",
+    "HECA",
+    "MAPKAPK2",
+    "C11orf58",
+    "IL2RB",
+    "GRK2",
+    "MTHFD2",
+    "KDM5C",
+    "SH2D1A",
+    "KIF5B",
+    "ITGB2",
+    "ARPC1B",
+    "UBE2A",
+    "TGFBR2",
+    "HOPX",
+    "MAPK6",
+    "ITK",
+    "PSMA7"
+   ],
+   "control_symbols_missing": [
+    "TOP3A",
+    "SFSWAP",
+    "NSRP1",
+    "CCDC115",
+    "BOD1L1",
+    "WDR75",
+    "BCL11B",
+    "YTHDC1",
+    "CHERP",
+    "NIFK",
+    "FARSB",
+    "PRPF19",
+    "COPB1"
+   ],
+   "n_control_symbols": 200,
+   "n_control_in_effect_universe": 187,
+   "control_ensembl": [
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+    "ENSG00000105701",
+    "ENSG00000128203",
+    "ENSG00000103148",
+    "ENSG00000173960",
+    "ENSG00000138175",
+    "ENSG00000138688",
+    "ENSG00000182463",
+    "ENSG00000186185",
+    "ENSG00000168056",
+    "ENSG00000186591",
+    "ENSG00000108479",
+    "ENSG00000214941",
+    "ENSG00000146833",
+    "ENSG00000132024",
+    "ENSG00000104884",
+    "ENSG00000173706",
+    "ENSG00000091732",
+    "ENSG00000163002",
+    "ENSG00000089057",
+    "ENSG00000198925",
+    "ENSG00000165240",
+    "ENSG00000000457",
+    "ENSG00000102007",
+    "ENSG00000108771",
+    "ENSG00000123575",
+    "ENSG00000104221",
+    "ENSG00000204178",
+    "ENSG00000138433",
+    "ENSG00000183155",
+    "ENSG00000135801",
+    "ENSG00000273559",
+    "ENSG00000149658",
+    "ENSG00000105135",
+    "ENSG00000156170",
+    "ENSG00000170234",
+    "ENSG00000189077",
+    "ENSG00000178188",
+    "ENSG00000164815",
+    "ENSG00000275835",
+    "ENSG00000103942",
+    "ENSG00000138942",
+    "ENSG00000109381",
+    "ENSG00000065970",
+    "ENSG00000119522",
+    "ENSG00000182372",
+    "ENSG00000112234",
+    "ENSG00000108799",
+    "ENSG00000110911",
+    "ENSG00000028116",
+    "ENSG00000196712",
+    "ENSG00000184162",
+    "ENSG00000170860",
+    "ENSG00000113272",
+    "ENSG00000152465",
+    "ENSG00000140598",
+    "ENSG00000033030",
+    "ENSG00000124532",
+    "ENSG00000026297",
+    "ENSG00000090857",
+    "ENSG00000164631",
+    "ENSG00000096433",
+    "ENSG00000204231",
+    "ENSG00000159231",
+    "ENSG00000173153",
+    "ENSG00000073803",
+    "ENSG00000171067",
+    "ENSG00000198692",
+    "ENSG00000132680",
+    "ENSG00000033327",
+    "ENSG00000146410",
+    "ENSG00000100330",
+    "ENSG00000175048",
+    "ENSG00000067369",
+    "ENSG00000140391",
+    "ENSG00000133641",
+    "ENSG00000101104",
+    "ENSG00000100379",
+    "ENSG00000113318",
+    "ENSG00000196943",
+    "ENSG00000138443",
+    "ENSG00000130150",
+    "ENSG00000169682",
+    "ENSG00000171425",
+    "ENSG00000149761",
+    "ENSG00000250317",
+    "ENSG00000100099",
+    "ENSG00000130699",
+    "ENSG00000214367",
+    "ENSG00000185298",
+    "ENSG00000197150",
+    "ENSG00000106003",
+    "ENSG00000110717",
+    "ENSG00000105793",
+    "ENSG00000198720",
+    "ENSG00000100632",
+    "ENSG00000196230",
+    "ENSG00000138768",
+    "ENSG00000101367",
+    "ENSG00000090061",
+    "ENSG00000166797",
+    "ENSG00000116062",
+    "ENSG00000101752",
+    "ENSG00000180776",
+    "ENSG00000119541",
+    "ENSG00000111790",
+    "ENSG00000125970",
+    "ENSG00000110200",
+    "ENSG00000100226",
+    "ENSG00000215788",
+    "ENSG00000225921",
+    "ENSG00000130402",
+    "ENSG00000171497",
+    "ENSG00000170776",
+    "ENSG00000175193",
+    "ENSG00000043093",
+    "ENSG00000161021",
+    "ENSG00000142186",
+    "ENSG00000072062",
+    "ENSG00000171843",
+    "ENSG00000136824",
+    "ENSG00000158604",
+    "ENSG00000104687",
+    "ENSG00000090554",
+    "ENSG00000066654",
+    "ENSG00000110852",
+    "ENSG00000131759",
+    "ENSG00000105393",
+    "ENSG00000171862",
+    "ENSG00000067066",
+    "ENSG00000164332",
+    "ENSG00000140575",
+    "ENSG00000136527",
+    "ENSG00000148688",
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+    "ENSG00000133030",
+    "ENSG00000102786",
+    "ENSG00000184182",
+    "ENSG00000038358",
+    "ENSG00000197771",
+    "ENSG00000145050",
+    "ENSG00000077420",
+    "ENSG00000275023",
+    "ENSG00000122034",
+    "ENSG00000163527",
+    "ENSG00000120686",
+    "ENSG00000161547",
+    "ENSG00000100714",
+    "ENSG00000186469",
+    "ENSG00000078596",
+    "ENSG00000074842",
+    "ENSG00000111335",
+    "ENSG00000102572",
+    "ENSG00000102471",
+    "ENSG00000163634",
+    "ENSG00000175768",
+    "ENSG00000112695",
+    "ENSG00000167792",
+    "ENSG00000072501",
+    "ENSG00000096384",
+    "ENSG00000109861",
+    "ENSG00000109971",
+    "ENSG00000189067",
+    "ENSG00000113384",
+    "ENSG00000138071",
+    "ENSG00000120438",
+    "ENSG00000169714",
+    "ENSG00000090487",
+    "ENSG00000104738",
+    "ENSG00000023445",
+    "ENSG00000112406",
+    "ENSG00000162889",
+    "ENSG00000110696",
+    "ENSG00000100385",
+    "ENSG00000173020",
+    "ENSG00000065911",
+    "ENSG00000126012",
+    "ENSG00000183918",
+    "ENSG00000170759",
+    "ENSG00000160255",
+    "ENSG00000130429",
+    "ENSG00000077721",
+    "ENSG00000163513",
+    "ENSG00000171476",
+    "ENSG00000069956",
+    "ENSG00000113263",
+    "ENSG00000101182"
+   ]
+  },
+  {
+   "program_id": "diff_activated",
+   "score_field": "diff_activated_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.2,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 5,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "CD69",
+    "IL2RA",
+    "CD38",
+    "MKI67",
+    "TNFRSF9"
+   ],
+   "panel_symbols_retained": [
+    "CD69",
+    "IL2RA",
+    "CD38",
+    "MKI67",
+    "TNFRSF9"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 5,
+   "n_panel_in_effect_universe": 5,
+   "panel_ensembl": [
+    "ENSG00000110848",
+    "ENSG00000134460",
+    "ENSG00000004468",
+    "ENSG00000148773",
+    "ENSG00000049249"
+   ],
+   "control_symbols_retained": [
+    "DCAF1",
+    "PLD6",
+    "COMMD4",
+    "GCLC",
+    "TMX4",
+    "DTNBP1",
+    "TANGO6",
+    "SOD1",
+    "HSPBP1",
+    "TMEM267",
+    "HEXB",
+    "RAD54B",
+    "AP4E1",
+    "HDAC8",
+    "WDR59",
+    "MADD",
+    "TMEM185A",
+    "ABHD18",
+    "MAST3",
+    "NDUFS5",
+    "IMMP2L",
+    "G2E3",
+    "MT1X",
+    "STK16",
+    "APEX2",
+    "SLC35F6",
+    "SLC35F2",
+    "NARF",
+    "SSNA1",
+    "CREG1",
+    "ZKSCAN1",
+    "ACTR6",
+    "CLASP2",
+    "ABCF3",
+    "GABPB2",
+    "ZNF580",
+    "PPME1",
+    "STX2",
+    "TOR1B",
+    "IDH1",
+    "FAM193B",
+    "CLUH",
+    "BRD8",
+    "NOL7",
+    "TMBIM1",
+    "ARMC10",
+    "EIF1B",
+    "SET",
+    "ZBTB25",
+    "BABAM1",
+    "FYTTD1",
+    "GIMAP5",
+    "SLC16A3",
+    "NSUN2",
+    "TMEM68",
+    "PEF1",
+    "PLRG1",
+    "ZFAND3",
+    "ACBD6",
+    "CSNK1D",
+    "CIB1",
+    "ARHGAP11A",
+    "PRDX3",
+    "RGCC",
+    "RHOH",
+    "ZYX",
+    "PITRM1",
+    "GFM1",
+    "DENR",
+    "PTTG1IP",
+    "TBC1D14",
+    "GGA2",
+    "MKLN1",
+    "KTN1",
+    "NCOR2",
+    "KLHL5",
+    "PARP14",
+    "TMBIM6",
+    "SNRNP25",
+    "RABEP1",
+    "AMD1",
+    "TMOD3",
+    "LRP8",
+    "WASHC3",
+    "PBX2",
+    "JOSD1",
+    "ERP44",
+    "RAP2B",
+    "SAE1",
+    "KAT6A",
+    "RAD50",
+    "ARF6",
+    "UBA3",
+    "SNRPB2",
+    "METAP2",
+    "SLAMF1",
+    "SSRP1",
+    "PSMA4",
+    "HNRNPU",
+    "H1-2",
+    "CAB39",
+    "PAK2",
+    "TUBA4A",
+    "PLEKHB2",
+    "ELOVL5",
+    "PPP1R9B",
+    "ARHGAP30",
+    "LCP1",
+    "CD2",
+    "UBE2D3",
+    "SRSF2",
+    "GOT2",
+    "GLRX3",
+    "SLC38A1",
+    "SCD",
+    "YWHAZ",
+    "HNRNPD",
+    "CAPNS1",
+    "ITK",
+    "EDEM1",
+    "ADD3",
+    "SMS",
+    "CD226",
+    "PSMD4",
+    "SDHB",
+    "FNBP1",
+    "DGKA",
+    "STT3B",
+    "BST2",
+    "UQCRC1",
+    "SAMHD1",
+    "HAPSTR1",
+    "FTL",
+    "NUCKS1",
+    "HNRNPUL2",
+    "PLCG1",
+    "ARHGEF2",
+    "EEF1B2",
+    "S100A10",
+    "SH3BGRL3"
+   ],
+   "control_symbols_missing": [
+    "UBAP1",
+    "PRPF18",
+    "POLA1",
+    "ZRANB1",
+    "COG4",
+    "CLCN7",
+    "CENPC",
+    "RACK1",
+    "PRPF6",
+    "PSMD13"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 140,
+   "control_ensembl": [
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+    "ENSG00000179598",
+    "ENSG00000140365",
+    "ENSG00000001084",
+    "ENSG00000125827",
+    "ENSG00000047579",
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+    "ENSG00000269556",
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+    "ENSG00000168653",
+    "ENSG00000184903",
+    "ENSG00000092140",
+    "ENSG00000187193",
+    "ENSG00000115661",
+    "ENSG00000169188",
+    "ENSG00000213699",
+    "ENSG00000110660",
+    "ENSG00000141562",
+    "ENSG00000176101",
+    "ENSG00000143162",
+    "ENSG00000106261",
+    "ENSG00000075089",
+    "ENSG00000163539",
+    "ENSG00000161204",
+    "ENSG00000143458",
+    "ENSG00000213015",
+    "ENSG00000214517",
+    "ENSG00000111450",
+    "ENSG00000136816",
+    "ENSG00000138413",
+    "ENSG00000146067",
+    "ENSG00000132361",
+    "ENSG00000112983",
+    "ENSG00000225921",
+    "ENSG00000135926",
+    "ENSG00000170632",
+    "ENSG00000114784",
+    "ENSG00000119335",
+    "ENSG00000089775",
+    "ENSG00000105393",
+    "ENSG00000122068",
+    "ENSG00000196329",
+    "ENSG00000141526",
+    "ENSG00000037474",
+    "ENSG00000167904",
+    "ENSG00000162517",
+    "ENSG00000171566",
+    "ENSG00000156639",
+    "ENSG00000230124",
+    "ENSG00000141551",
+    "ENSG00000185043",
+    "ENSG00000198826",
+    "ENSG00000165672",
+    "ENSG00000102760",
+    "ENSG00000168421",
+    "ENSG00000159840",
+    "ENSG00000107959",
+    "ENSG00000168827",
+    "ENSG00000139726",
+    "ENSG00000183255",
+    "ENSG00000132405",
+    "ENSG00000103365",
+    "ENSG00000128585",
+    "ENSG00000126777",
+    "ENSG00000196498",
+    "ENSG00000109790",
+    "ENSG00000173193",
+    "ENSG00000139644",
+    "ENSG00000161981",
+    "ENSG00000029725",
+    "ENSG00000123505",
+    "ENSG00000138594",
+    "ENSG00000157193",
+    "ENSG00000120860",
+    "ENSG00000204304",
+    "ENSG00000100221",
+    "ENSG00000023318",
+    "ENSG00000181467",
+    "ENSG00000142230",
+    "ENSG00000083168",
+    "ENSG00000113522",
+    "ENSG00000165527",
+    "ENSG00000144744",
+    "ENSG00000125870",
+    "ENSG00000111142",
+    "ENSG00000117090",
+    "ENSG00000149136",
+    "ENSG00000041357",
+    "ENSG00000153187",
+    "ENSG00000187837",
+    "ENSG00000135932",
+    "ENSG00000180370",
+    "ENSG00000127824",
+    "ENSG00000115762",
+    "ENSG00000012660",
+    "ENSG00000108819",
+    "ENSG00000186517",
+    "ENSG00000136167",
+    "ENSG00000116824",
+    "ENSG00000109332",
+    "ENSG00000161547",
+    "ENSG00000125166",
+    "ENSG00000108010",
+    "ENSG00000111371",
+    "ENSG00000099194",
+    "ENSG00000164924",
+    "ENSG00000138668",
+    "ENSG00000126247",
+    "ENSG00000113263",
+    "ENSG00000134109",
+    "ENSG00000148700",
+    "ENSG00000102172",
+    "ENSG00000150637",
+    "ENSG00000159352",
+    "ENSG00000117118",
+    "ENSG00000187239",
+    "ENSG00000065357",
+    "ENSG00000163527",
+    "ENSG00000130303",
+    "ENSG00000010256",
+    "ENSG00000101347",
+    "ENSG00000182831",
+    "ENSG00000087086",
+    "ENSG00000069275",
+    "ENSG00000214753",
+    "ENSG00000124181",
+    "ENSG00000116584",
+    "ENSG00000114942",
+    "ENSG00000197747",
+    "ENSG00000142669"
+   ]
+  },
+  {
+   "program_id": "diff_memory",
+   "score_field": "diff_memory_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.1666666667,
+    "control_coef": -0.0066666667,
+    "n_measured_panel": 6,
+    "n_control": 150
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "ITGAL",
+    "FAS",
+    "CD58",
+    "ITGA4",
+    "S100A4",
+    "CD27"
+   ],
+   "panel_symbols_retained": [
+    "ITGAL",
+    "FAS",
+    "CD58",
+    "ITGA4",
+    "S100A4",
+    "CD27"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 6,
+   "n_panel_in_effect_universe": 6,
+   "panel_ensembl": [
+    "ENSG00000005844",
+    "ENSG00000026103",
+    "ENSG00000116815",
+    "ENSG00000115232",
+    "ENSG00000196154",
+    "ENSG00000139193"
+   ],
+   "control_symbols_retained": [
+    "SP1",
+    "REST",
+    "PNO1",
+    "IFT57",
+    "TIMMDC1",
+    "AFG3L2",
+    "NR3C1",
+    "SAMD1",
+    "FNBP4",
+    "DDX50",
+    "TBK1",
+    "FOXO1",
+    "RC3H2",
+    "ATRX",
+    "OARD1",
+    "SMIM26",
+    "CARS2",
+    "SNUPN",
+    "INCENP",
+    "ATXN1",
+    "ASCC2",
+    "SLC12A7",
+    "STAT5A",
+    "SNX12",
+    "CHEK1",
+    "SENP1",
+    "GLUD1",
+    "DTYMK",
+    "DHCR24",
+    "MPDU1",
+    "EPSTI1",
+    "IDH3G",
+    "TMEM259",
+    "HIPK1",
+    "GRAMD1A",
+    "P2RX4",
+    "DMTF1",
+    "ITPK1",
+    "SNX4",
+    "GIT1",
+    "ZEB1",
+    "LAMTOR5",
+    "FXN",
+    "YEATS4",
+    "GMFG",
+    "NRAS",
+    "MIER1",
+    "SLC25A11",
+    "YWHAE",
+    "SYNRG",
+    "HIGD2A",
+    "KIF21B",
+    "RAB8B",
+    "ELOC",
+    "ADAM8",
+    "EHMT1",
+    "STAU2",
+    "HPRT1",
+    "PPP6C",
+    "SNRPE",
+    "SRSF4",
+    "SRA1",
+    "ADSS2",
+    "CANX",
+    "RNF10",
+    "ZFP36L2",
+    "ECE1",
+    "NUP50",
+    "KCTD20",
+    "ZBTB1",
+    "SEC61A1",
+    "CHMP4A",
+    "HK1",
+    "KDM2A",
+    "KLF2",
+    "BIN2",
+    "MBNL1",
+    "DPM1",
+    "TERF2IP",
+    "BLOC1S1",
+    "KPNA4",
+    "SLC7A5",
+    "GNPTAB",
+    "EIF2AK2",
+    "NUP153",
+    "CARM1",
+    "GSTO1",
+    "TOP2A",
+    "NOP10",
+    "CELF1",
+    "ID2",
+    "OSTF1",
+    "TMEM123",
+    "UBE2I",
+    "KCNAB2",
+    "CD44",
+    "ABRACL",
+    "HSP90AB1",
+    "CELF2",
+    "NDUFA4",
+    "FAM120A",
+    "UBAP2L",
+    "IFI16",
+    "DUS1L",
+    "SUMF2",
+    "ARPC2",
+    "CD47",
+    "PRRC2C",
+    "ILF2",
+    "STT3B",
+    "TMEM167A",
+    "S100A10",
+    "CNN2",
+    "GNG2",
+    "LRPPRC",
+    "TANK",
+    "WIPF1",
+    "CAPN2",
+    "SATB1",
+    "CCT8",
+    "UBXN4",
+    "C11orf58",
+    "PRPF40A",
+    "HSPH1",
+    "MYH9",
+    "HNRNPUL2",
+    "RHOG",
+    "COPA",
+    "H1-5",
+    "PPP1CA",
+    "PAFAH1B1",
+    "ATF2",
+    "ARID5B",
+    "EFCAB14",
+    "SLTM",
+    "NDUFB9",
+    "COX8A",
+    "WDR26"
+   ],
+   "control_symbols_missing": [
+    "CEBPZOS",
+    "RBM22",
+    "PLSCR3",
+    "ARHGEF3",
+    "NUP155",
+    "TERF2",
+    "SF3B4",
+    "TSR1",
+    "NUP62",
+    "NUP58",
+    "B2M",
+    "EBNA1BP2"
+   ],
+   "n_control_symbols": 150,
+   "n_control_in_effect_universe": 138,
+   "control_ensembl": [
+    "ENSG00000185591",
+    "ENSG00000084093",
+    "ENSG00000115946",
+    "ENSG00000114446",
+    "ENSG00000113845",
+    "ENSG00000141385",
+    "ENSG00000113580",
+    "ENSG00000141858",
+    "ENSG00000109920",
+    "ENSG00000107625",
+    "ENSG00000183735",
+    "ENSG00000150907",
+    "ENSG00000056586",
+    "ENSG00000085224",
+    "ENSG00000124596",
+    "ENSG00000232388",
+    "ENSG00000134905",
+    "ENSG00000169371",
+    "ENSG00000149503",
+    "ENSG00000124788",
+    "ENSG00000100325",
+    "ENSG00000113504",
+    "ENSG00000126561",
+    "ENSG00000147164",
+    "ENSG00000149554",
+    "ENSG00000079387",
+    "ENSG00000148672",
+    "ENSG00000168393",
+    "ENSG00000116133",
+    "ENSG00000129255",
+    "ENSG00000133106",
+    "ENSG00000067829",
+    "ENSG00000182087",
+    "ENSG00000163349",
+    "ENSG00000089351",
+    "ENSG00000135124",
+    "ENSG00000135164",
+    "ENSG00000100605",
+    "ENSG00000114520",
+    "ENSG00000108262",
+    "ENSG00000148516",
+    "ENSG00000134248",
+    "ENSG00000165060",
+    "ENSG00000127337",
+    "ENSG00000130755",
+    "ENSG00000213281",
+    "ENSG00000198160",
+    "ENSG00000108528",
+    "ENSG00000108953",
+    "ENSG00000275066",
+    "ENSG00000146066",
+    "ENSG00000116852",
+    "ENSG00000166128",
+    "ENSG00000154582",
+    "ENSG00000151651",
+    "ENSG00000181090",
+    "ENSG00000040341",
+    "ENSG00000165704",
+    "ENSG00000119414",
+    "ENSG00000182004",
+    "ENSG00000116350",
+    "ENSG00000213523",
+    "ENSG00000035687",
+    "ENSG00000127022",
+    "ENSG00000022840",
+    "ENSG00000152518",
+    "ENSG00000117298",
+    "ENSG00000093000",
+    "ENSG00000112078",
+    "ENSG00000126804",
+    "ENSG00000058262",
+    "ENSG00000254505",
+    "ENSG00000156515",
+    "ENSG00000173120",
+    "ENSG00000127528",
+    "ENSG00000110934",
+    "ENSG00000152601",
+    "ENSG00000000419",
+    "ENSG00000166848",
+    "ENSG00000135441",
+    "ENSG00000186432",
+    "ENSG00000103257",
+    "ENSG00000111670",
+    "ENSG00000055332",
+    "ENSG00000124789",
+    "ENSG00000142453",
+    "ENSG00000148834",
+    "ENSG00000131747",
+    "ENSG00000182117",
+    "ENSG00000149187",
+    "ENSG00000115738",
+    "ENSG00000134996",
+    "ENSG00000152558",
+    "ENSG00000103275",
+    "ENSG00000069424",
+    "ENSG00000026508",
+    "ENSG00000146386",
+    "ENSG00000096384",
+    "ENSG00000048740",
+    "ENSG00000189043",
+    "ENSG00000048828",
+    "ENSG00000143569",
+    "ENSG00000163565",
+    "ENSG00000169718",
+    "ENSG00000129103",
+    "ENSG00000163466",
+    "ENSG00000196776",
+    "ENSG00000117523",
+    "ENSG00000143621",
+    "ENSG00000163527",
+    "ENSG00000174695",
+    "ENSG00000197747",
+    "ENSG00000064666",
+    "ENSG00000186469",
+    "ENSG00000138095",
+    "ENSG00000136560",
+    "ENSG00000115935",
+    "ENSG00000162909",
+    "ENSG00000182568",
+    "ENSG00000156261",
+    "ENSG00000144224",
+    "ENSG00000110696",
+    "ENSG00000196504",
+    "ENSG00000120694",
+    "ENSG00000100345",
+    "ENSG00000214753",
+    "ENSG00000177105",
+    "ENSG00000122218",
+    "ENSG00000184357",
+    "ENSG00000172531",
+    "ENSG00000007168",
+    "ENSG00000115966",
+    "ENSG00000150347",
+    "ENSG00000159658",
+    "ENSG00000137776",
+    "ENSG00000147684",
+    "ENSG00000176340",
+    "ENSG00000162923"
+   ]
+  },
+  {
+   "program_id": "diff_checkpoint",
+   "score_field": "diff_checkpoint_score",
+   "role": "primary",
+   "primary": true,
+   "base_portable": true,
+   "scoring_method": "deterministic expression-bin-matched panel-minus-control",
+   "normalization": "median_total\u22489819 + log1p (from .X; no raw layer)",
+   "coefficients": {
+    "panel_coef": 0.1666666667,
+    "control_coef": -0.004,
+    "n_measured_panel": 6,
+    "n_control": 250
+   },
+   "n_bins": 25,
+   "ctrl_size": 50,
+   "panel_symbols": [
+    "PDCD1",
+    "TOX",
+    "HAVCR2",
+    "LAG3",
+    "TIGIT",
+    "ENTPD1"
+   ],
+   "panel_symbols_retained": [
+    "PDCD1",
+    "TOX",
+    "HAVCR2",
+    "LAG3",
+    "TIGIT",
+    "ENTPD1"
+   ],
+   "panel_symbols_missing": [],
+   "n_panel_symbols": 6,
+   "n_panel_in_effect_universe": 6,
+   "panel_ensembl": [
+    "ENSG00000188389",
+    "ENSG00000198846",
+    "ENSG00000135077",
+    "ENSG00000089692",
+    "ENSG00000181847",
+    "ENSG00000138185"
+   ],
+   "control_symbols_retained": [
+    "RAB43",
+    "C1QTNF6",
+    "NECTIN1",
+    "RFX2",
+    "KRTCAP3",
+    "ZBTB12",
+    "TOR2A",
+    "ZRANB3",
+    "ZNF2",
+    "ZNF772",
+    "EGFL6",
+    "SERPINI1",
+    "PWWP2B",
+    "H2AC8",
+    "ZNF579",
+    "SLC16A5",
+    "CCDC120",
+    "ANKS6",
+    "GJB6",
+    "CASS4",
+    "ZNF250",
+    "MT1E",
+    "WHRN",
+    "TMEM217",
+    "CNOT7",
+    "FHL1",
+    "STOX1",
+    "FAM104A",
+    "SEMA4F",
+    "GMPR",
+    "SPATC1L",
+    "ARHGEF11",
+    "SLC17A9",
+    "TESK2",
+    "CAPN12",
+    "REEP2",
+    "RWDD2A",
+    "ABITRAM",
+    "ADM5",
+    "PELI3",
+    "RIBC2",
+    "ZBTB43",
+    "POPDC2",
+    "ZNF649",
+    "RPGR",
+    "GNG8",
+    "RXRA",
+    "ZNF430",
+    "CHI3L2",
+    "LIN37",
+    "ADCY9",
+    "CNNM2",
+    "FKRP",
+    "ZNF714",
+    "IFIT3",
+    "KCTD3",
+    "NCS1",
+    "KCNQ5",
+    "ZFP82",
+    "ZNF736",
+    "CARD6",
+    "ZNF408",
+    "CCDC152",
+    "TRIM34",
+    "PLXNB2",
+    "TUBA1A",
+    "ABHD11",
+    "FASTKD3",
+    "VWA5A",
+    "GNAI1",
+    "KCTD18",
+    "NCKAP1",
+    "PPP1R3F",
+    "ZNF626",
+    "ZNF155",
+    "TTBK2",
+    "TMTC4",
+    "TYSND1",
+    "OAT",
+    "ZFYVE26",
+    "H6PD",
+    "SETMAR",
+    "BTLA",
+    "ZBTB34",
+    "IPCEF1",
+    "KYAT1",
+    "FAM117B",
+    "KIAA0513",
+    "ZNF717",
+    "H1-0",
+    "ZNF358",
+    "WHAMM",
+    "FAM120C",
+    "CEP19",
+    "TRMT11",
+    "SWI5",
+    "TMLHE",
+    "CRADD",
+    "ACSS1",
+    "ALKBH8",
+    "RECQL4",
+    "SSX2IP",
+    "AOAH",
+    "DOP1B",
+    "NCR3",
+    "RECQL5",
+    "FTO",
+    "VKORC1L1",
+    "PSMD5",
+    "BSCL2",
+    "MED19",
+    "ZNF480",
+    "MAPKBP1",
+    "CRYZL1",
+    "ARHGEF9",
+    "GANC",
+    "MED16",
+    "VGLL4",
+    "PRIMPOL",
+    "MRM3",
+    "REEP4",
+    "ERI2",
+    "ZMYM6",
+    "NANP",
+    "EFCAB11",
+    "GEMIN2",
+    "PKP4",
+    "ZNF436",
+    "G6PC3",
+    "MCU",
+    "CC2D1B",
+    "SLC35B3",
+    "ATG10",
+    "ZNF641",
+    "CAPRIN2",
+    "TIMM17B",
+    "SLC41A2",
+    "KEAP1",
+    "DCUN1D1",
+    "PPP2R5D",
+    "IFITM2",
+    "HAPLN3",
+    "SP140L",
+    "HMOX2",
+    "RABGAP1L",
+    "GNL2",
+    "NDUFB1",
+    "NLRC5",
+    "ERP44",
+    "MIS18BP1",
+    "IFNAR2",
+    "WDR18",
+    "GGNBP2",
+    "DNAJB11",
+    "NCAPD3",
+    "TIA1",
+    "KAT6A",
+    "ACTN4",
+    "UCHL5",
+    "MGAT4B",
+    "ITM2C",
+    "DCTN2",
+    "ZBTB25",
+    "SUGT1",
+    "WAPL",
+    "MEX3C",
+    "POLR3K",
+    "ARHGAP11A",
+    "GZMA",
+    "ZDHHC18",
+    "DDOST",
+    "BCAS2",
+    "MPRIP",
+    "TMEM208",
+    "PRKCA",
+    "TAGLN2",
+    "AKT2",
+    "DUSP5",
+    "RRP36",
+    "KMT2E",
+    "CGAS",
+    "DOT1L",
+    "LRRC59",
+    "UBB",
+    "RNF167",
+    "CCL4",
+    "SIN3A",
+    "CIAO2B",
+    "IDH3B",
+    "LSM7",
+    "RBM33",
+    "PTK2B",
+    "NSD1",
+    "C1QBP",
+    "SQOR",
+    "DEGS1",
+    "DNMT1",
+    "ECH1",
+    "PDCD6",
+    "TRAPPC4",
+    "ZC3H4",
+    "BPNT2",
+    "PSMB10",
+    "EED",
+    "SLA",
+    "PSMB5",
+    "DAZAP1",
+    "GTF2E2",
+    "RABL6",
+    "RBL2",
+    "UBA2",
+    "EML4",
+    "DPM1",
+    "GID8",
+    "CWC15",
+    "EIF3K",
+    "PPP1R15B",
+    "SPCS3",
+    "RASSF3",
+    "SYNE3",
+    "ODC1",
+    "SEM1",
+    "SND1",
+    "USP48",
+    "ORMDL1",
+    "TBC1D2B",
+    "URI1"
+   ],
+   "control_symbols_missing": [
+    "USP54",
+    "ROM1",
+    "FTCDNL1",
+    "ELMO3",
+    "SIPA1L2",
+    "THBS4",
+    "C2orf72",
+    "GEMIN8",
+    "GPATCH1",
+    "STX18",
+    "GINS4",
+    "WDR1",
+    "ATRIP",
+    "ASCC3",
+    "SLU7",
+    "SRRT",
+    "NIFK",
+    "GUK1",
+    "YTHDC1",
+    "NOP14",
+    "NUP58",
+    "MACF1",
+    "SF3A2"
+   ],
+   "n_control_symbols": 250,
+   "n_control_in_effect_universe": 227,
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+    "ENSG00000133466",
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+    "ENSG00000087903",
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+    "ENSG00000154930",
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+    "ENSG00000117155",
+    "ENSG00000136250",
+    "ENSG00000142197",
+    "ENSG00000204475",
+    "ENSG00000108469",
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+    "ENSG00000095261",
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+    "ENSG00000156603",
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+    "ENSG00000249915",
+    "ENSG00000196655",
+    "ENSG00000130749",
+    "ENSG00000104331",
+    "ENSG00000205220",
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+    "ENSG00000100804",
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+    "ENSG00000000419",
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+    "ENSG00000090686",
+    "ENSG00000128699",
+    "ENSG00000167202",
+    "ENSG00000105176"
+   ]
+  }
+ ]
+}

stage1-continuous-v3.0.1/receipts/stage01_v3_recovery_verification.json

@@ -0,0 +1,220 @@
+{
+ "schema": "spot.stage01_v3_recovery_verification.v1",
+ "method_version": "stage1-continuous-v3.0.1",
+ "parquet_shape": [
+  396000,
+  15
+ ],
+ "columns": [
+  "barcode",
+  "donor",
+  "condition",
+  "th1_like_score",
+  "th2_like_score",
+  "th17_like_score",
+  "tfh_like_score",
+  "treg_like_score",
+  "cd4_ctl_like_score",
+  "th9_like_score",
+  "diff_naive_score",
+  "diff_activated_score",
+  "diff_memory_score",
+  "diff_checkpoint_score",
+  "cd4_ctl_like_score_actadj"
+ ],
+ "checks": {
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+   "target": "43c4296d5166740c334441a69df23bb440a073382bbe79628a3bb89e43d51316",
+   "match": true,
+   "score_fields": [
+    "th1_like_score",
+    "th2_like_score",
+    "th17_like_score",
+    "tfh_like_score",
+    "treg_like_score",
+    "cd4_ctl_like_score",
+    "th9_like_score",
+    "diff_naive_score",
+    "diff_activated_score",
+    "diff_memory_score",
+    "diff_checkpoint_score",
+    "cd4_ctl_like_score_actadj"
+   ],
+   "n_rows": 396000
+  },
+  "overlay_equals_full": {
+   "n_overlay": 40000,
+   "mismatches": 0,
+   "overlay_eq_full_all_fields": true,
+   "barcodes_all_present": true
+  },
+  "controls": {
+   "committed_csv_rows": 2100,
+   "registry_11_programs_total": 1950,
+   "csv_11_programs_total": 1950,
+   "all_programs_symbol_multiset_match": true,
+   "per_program": {
+    "th1_like": {
+     "registry_n": 150,
+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
+    "th2_like": {
+     "registry_n": 150,
+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
+    "th17_like": {
+     "registry_n": 150,
+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
+    "tfh_like": {
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+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
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+     "csv_n": 250,
+     "symbol_multiset_match": true
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+     "csv_n": 250,
+     "symbol_multiset_match": true
+    },
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+     "csv_n": 100,
+     "symbol_multiset_match": true
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+     "csv_n": 200,
+     "symbol_multiset_match": true
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+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
+    "diff_memory": {
+     "registry_n": 150,
+     "csv_n": 150,
+     "symbol_multiset_match": true
+    },
+    "diff_checkpoint": {
+     "registry_n": 250,
+     "csv_n": 250,
+     "symbol_multiset_match": true
+    }
+   },
+   "note": "CSV also carries the sensitivity/activation lane program_id(s) ['activation_predictor'] (not in registry programs[]); those account for the CSV rows beyond the 11 primaries."
+  },
+  "summary_regenerated": {
+   "n_program_condition_strata_compared": 36,
+   "n_exact_at_5dp": 25,
+   "n_within_1ulp_at_5dp": 36,
+   "max_abs_deviation_vs_candidate": 1.0000000000010001e-05,
+   "median_iqr_mad_all_match": true,
+   "note": "Regenerated by_program_condition (median/iqr/mad) directly from the 396k parquet under v3.0.1. Agreement with the candidate summary is exact to 4dp; the residual is <=1 unit in the last (5th) stored decimal (percentile-interpolation / even-length-median ULP), reported as max_abs_deviation."
+  },
+  "coefficient_internal_consistency": {
+   "all_consistent": true,
+   "detail": [
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+     "n_measured_panel": 4,
+     "n_panel_genes_measured": 4,
+     "n_measured_panel_matches": true
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+     "program_id": "th2_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 4,
+     "n_panel_genes_measured": 4,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "th17_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 6,
+     "n_panel_genes_measured": 6,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "tfh_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 3,
+     "n_panel_genes_measured": 3,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "treg_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 5,
+     "n_panel_genes_measured": 5,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "cd4_ctl_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 6,
+     "n_panel_genes_measured": 6,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "th9_like",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 2,
+     "n_panel_genes_measured": 2,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "diff_naive",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 6,
+     "n_panel_genes_measured": 6,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "diff_activated",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 5,
+     "n_panel_genes_measured": 5,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "diff_memory",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 6,
+     "n_panel_genes_measured": 6,
+     "n_measured_panel_matches": true
+    },
+    {
+     "program_id": "diff_checkpoint",
+     "panel_coef_finite": true,
+     "control_coef_finite": true,
+     "n_measured_panel": 6,
+     "n_panel_genes_measured": 6,
+     "n_measured_panel_matches": true
+    }
+   ],
+   "note": "Coefficients are finite scalar weights (panel_coef/control_coef) and n_measured_panel matches len(panel_genes_measured). Recomputing coefficients from the frozen method requires the pinned h5ad and is done by the scoring-tier reproduce, not here."
+  }
+ },
+ "all_pass": true
+}

stage1-continuous-v3.0.1/validation/stage01_gate_constituents_overlay_donor_v1.json.gz

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stage1-continuous-v3.0.1/validation/stage01_gate_constituents_overlay_donor_v1.manifest.json

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+  "note": "Companion definedness evidence for the two non-production ratio metrics whose aggregates the deleted zero-value heuristic mislabels. value:null iff denom IQR==0.",
+  "row_count": 264,
+  "schema": "spot.stage01_gate_constituents_overlay_donor.manifest.v1",
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+}

stage1-continuous-v3.0.1/validation/stage01_gate_constituents_v1.json.gz

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stage1-continuous-v3.0.1/validation/stage01_gate_constituents_v1.manifest.json

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+  "integrity": {
+    "control_redraw_matches_committed": true,
+    "primary_score_exact_after_5dp_round": true,
+    "primary_score_maxerr_preround": 4.999999999949489e-06
+  },
+  "json_mirror": "stage01_gate_constituents_v1.json.gz",
+  "method_version": "stage1-continuous-v3.0.1",
+  "parquet_raw_sha256": "8bdce731c810b3519fb14e290847a6d130f4bc8a94b999916fa022c2bc1b4b57",
+  "row_count": 6849,
+  "schema": "spot.stage01_gate_constituents.manifest.v1",
+  "sort_key": [
+    "gate_class",
+    "gate_family",
+    "subcheck_id",
+    "program_id",
+    "condition",
+    "donor",
+    "removed_marker",
+    "alt_seed"
+  ]
+}

stage1-continuous-v3.0.1/validation/stage01_gate_constituents_v1.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8bdce731c810b3519fb14e290847a6d130f4bc8a94b999916fa022c2bc1b4b57
+size 92055

stage1-continuous-v3.0.1/validation/stage01_gate_spec.json

@@ -0,0 +1,106 @@
+{
+  "schema": "spot.stage01_gate_spec.v2",
+  "method_version": "stage1-continuous-v3",
+  "pre_registered": true,
+  "authored_before_scores": true,
+  "framing": "Frozen engineering/QC tolerances, NOT inferential cutoffs. No p-values, no FDR.",
+  "principles": [
+    "scale-aware: no cross-program raw-median comparison (A/B are on different scales)",
+    "membership-free: no zero-origin sign test, no above-median cell membership",
+    "stage1_selectable_by_condition stored per condition, not one global boolean",
+    "stage2_base_portability kept separate from stage-1 measurement validity",
+    "396k cells are not biological replicates",
+    "on failure: record nonselectable for that condition; do NOT retune markers/seeds/thresholds afterward"
+  ],
+  "implementation": {
+    "spearman": {"ranks": "average", "cells": "finite_only", "p_value": false},
+    "iqr": {"formula": "Q75 - Q25", "quantile_method": "numpy_linear"},
+    "hard_gate_undefined": {"iqr_zero": "fail", "undefined_correlation": "fail"},
+    "pair_and_offaxis_conditions": ["Rest", "Stim8hr", "Stim48hr"],
+    "pair_and_offaxis_note": "run for all three real conditions, NOT a post-selection 'selected condition'",
+    "overlay_standardized_error": "abs(median_overlay - median_full) / IQR_full <= 0.10",
+    "no_reseed_resample_substitute": true,
+    "emit_every_failure": "T7b emits every failure as-is; no reseeding, resampling, or marker substitution",
+    "result_record_fields": ["gate_id", "stratum_instance", "metric", "observed_value", "operator", "threshold", "pass", "worst_donor", "worst_marker", "worst_seed", "consequence"]
+  },
+  "overlay_expected_counts": {
+    "D1|Rest": 3420, "D1|Stim8hr": 3273, "D1|Stim48hr": 3294,
+    "D2|Rest": 3305, "D2|Stim8hr": 3442, "D2|Stim48hr": 3372,
+    "D3|Rest": 3270, "D3|Stim8hr": 3323, "D3|Stim48hr": 3317,
+    "D4|Rest": 3336, "D4|Stim8hr": 3286, "D4|Stim48hr": 3362,
+    "TOTAL": 40000
+  },
+  "control_draw_alt_seeds": [12346, 12347, 12348, 12349, 12350, 12351, 12352, 12353, 12354, 12355, 12356, 12357, 12358, 12359, 12360, 12361, 12362, 12363, 12364, 12365],
+  "gates": [
+    {"id": "global_coverage", "stratum": "program", "rule": "n_panel_genes_used >= 3",
+     "checks": [{"metric": "n_panel_genes_used", "operator": ">=", "threshold": 3, "aggregation": "single", "conditions": null, "equality": "inclusive", "undefined": "fail", "consequence": "program_globally_nonselectable"}]},
+
+    {"id": "stage2_base_portability", "stratum": "program",
+     "rule": "n_panel_in_effect_universe >= 3 AND n_control_in_effect_universe >= 10; record retained panel/control coefficient fractions",
+     "records": ["retained_panel_coefficient_fraction", "retained_control_coefficient_fraction"],
+     "note": "separate from stage-1 measurement validity; target-specific masking remains a stage-2 gate",
+     "checks": [
+       {"metric": "n_panel_in_effect_universe", "operator": ">=", "threshold": 3, "aggregation": "single", "conditions": null, "equality": "inclusive", "undefined": "fail", "consequence": "stage2_unavailable"},
+       {"metric": "n_control_in_effect_universe", "operator": ">=", "threshold": 10, "aggregation": "single", "conditions": null, "equality": "inclusive", "undefined": "fail", "consequence": "stage2_unavailable"}
+     ]},
+
+    {"id": "condition_measurability", "stratum": "program x condition x donor",
+     "rule": "in every donor at condition C: panel-score IQR > 0 AND >=2 panel genes detected in >=1% of cells",
+     "checks": [
+       {"metric": "panel_score_iqr", "operator": ">", "threshold": 0, "aggregation": "all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "exclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"},
+       {"metric": "n_panel_genes_detected_ge_1pct_cells", "operator": ">=", "threshold": 2, "aggregation": "all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"}
+     ]},
+
+    {"id": "lomo_panel_robustness", "stratum": "program x condition x removed_marker x donor",
+     "rule": "controls FIXED; compare panel_mean_full vs panel_mean_minus_gene (NOT the control-sharing scores)",
+     "checks": [
+       {"metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)", "operator": ">=", "threshold": 0.80, "aggregation": "all_markers_all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"},
+       {"metric": "median(abs(delta_panel))/iqr(panel_mean_full)", "operator": "<=", "threshold": 0.25, "aggregation": "all_markers_all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"}
+     ]},
+
+    {"id": "control_draw_sensitivity", "stratum": "program x condition x seed x donor",
+     "rule": "20 alt master seeds (control_draw_alt_seeds); for every seed and donor x condition",
+     "checks": [
+       {"metric": "spearman_rho(score_primary, score_alt_seed)", "operator": ">=", "threshold": 0.90, "aggregation": "all_seeds_all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"},
+       {"metric": "abs(median_alt - median_primary)/iqr_primary", "operator": "<=", "threshold": 0.25, "aggregation": "all_seeds_all_donors", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "program_condition_nonselectable"}
+     ]},
+
+    {"id": "selection_preflight", "stratum": "selection",
+     "rule": "structural gate at selection time",
+     "structural_conditions": ["both_programs_selectable_at_condition", "same_real_condition", "all_four_donors", "no_sensitivity_lane", "not_all_times", "A_program_or_direction_differs_from_B"],
+     "checks": [{"metric": "structural_preflight_all_true", "operator": "==", "threshold": true, "aggregation": "all", "conditions": null, "equality": "exact", "undefined": "fail", "consequence": "reject_selection"}]},
+
+    {"id": "pair_redundancy", "stratum": "pair x donor x condition", "advisory": true,
+     "rule": "per-donor Spearman rho(A,B) in EACH real condition; pair_redundant if |rho| >= 0.90 in >=3 of 4 donors (per condition); store all four signed rho per condition",
+     "checks": [{"metric": "abs(spearman_rho(A,B))", "operator": ">=", "threshold": 0.90, "aggregation": "donor_consensus_ge_3_of_4", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "not_evaluable", "consequence": "flag_pair_redundant"}],
+     "records": ["signed_rho_per_donor_per_condition"]},
+
+    {"id": "off_axis_association", "stratum": "axis x program_C x donor x condition", "advisory": true,
+     "rule": "for every other evaluable primary program C: per-donor rho(A,C) and rho(B,C) separately in EACH real condition; exclude sensitivity lanes; never construct A-B",
+     "exclude_sensitivity_lanes": true, "never_construct_A_minus_B": true,
+     "checks": [{"metric": "abs(spearman_rho(axis_program, C))", "operator": ">=", "threshold": 0.90, "aggregation": "donor_consensus_ge_3_of_4", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "not_evaluable", "consequence": "record_off_axis_association"}]},
+
+    {"id": "overlay_composition", "stratum": "overlay",
+     "rule": "EXACT frozen donor x condition barcode counts (see overlay_expected_counts)",
+     "checks": [{"metric": "donor_condition_counts", "operator": "==", "threshold": "overlay_expected_counts", "aggregation": "all_cells", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "exact", "undefined": "fail", "consequence": "block_overlay_release"}]},
+
+    {"id": "overlay_distributions", "stratum": "program x donor x condition",
+     "rule": "IQR-standardized median error <= 0.10 AND ECDF sup-distance D <= 0.05 (no KS p-value)",
+     "checks": [
+       {"metric": "abs(median_overlay - median_full)/iqr_full", "operator": "<=", "threshold": 0.10, "aggregation": "all", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "block_overlay_release"},
+       {"metric": "ecdf_sup_distance_D(overlay, full)", "operator": "<=", "threshold": 0.05, "aggregation": "all", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "block_overlay_release"}
+     ]},
+
+    {"id": "overlay_correlations", "stratum": "condition",
+     "rule": "per condition: max pairwise Spearman difference between overlay and full data <= 0.10",
+     "checks": [{"metric": "max_pairwise_spearman_diff(overlay, full)", "operator": "<=", "threshold": 0.10, "aggregation": "all_pairs", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "inclusive", "undefined": "fail", "consequence": "block_overlay_release"}]},
+
+    {"id": "donor_sensitivity", "stratum": "program x condition", "advisory": true,
+     "rule": "max_LODO abs(median_3donor - median_4donor)/iqr_4donor > 0.25 -> flag",
+     "checks": [{"metric": "max_lodo(abs(median_3donor - median_4donor)/iqr_4donor)", "operator": ">", "threshold": 0.25, "aggregation": "max_over_lodo_folds", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": "exclusive", "undefined": "not_evaluable", "consequence": "flag_donor_sensitive"}]},
+
+    {"id": "cp10k_v2_comparison", "stratum": "program", "descriptive": true,
+     "rule": "report stratified rank concordance + IQR-standardized shifts",
+     "checks": [{"metric": "stratified_rank_concordance_and_iqr_std_shift", "operator": "report", "threshold": null, "aggregation": "report", "conditions": ["Rest", "Stim8hr", "Stim48hr"], "equality": null, "undefined": "not_evaluable", "consequence": "descriptive_only"}]}
+  ]
+}

stage1-continuous-v3.0.1/validation/stage01_selectability_v3.json

@@ -0,0 +1,1577 @@
+{
+  "schema": "spot.stage01_selectability_v3.v2",
+  "method_version": "stage1-continuous-v3.0.1",
+  "derivation": "Deterministically derived from the immutable T7b validation (bound by raw sha below) via stage1_t8_derive. No retuning; a false hard-gate is never reinterpreted as advisory. failed_or_undefined_hard_gates is a MULTISET (a gate failing in two strata appears twice).",
+  "production_selectable_default": false,
+  "n_records": 33,
+  "n_production_selectable_true": 0,
+  "n_selectable_program_conditions": 0,
+  "portability_disclaimer": "stage2_base_portability is a SEPARATE necessary condition and DOES NOT confer stage-1 production selectability. No current program-condition pair cleared the frozen production gate.",
+  "not_a_biological_invalidity_claim": "This records only that no current program-condition pair cleared the frozen production gate; it does not assert any program is biologically invalid.",
+  "bound_hashes": {
+    "validation_raw_sha256": "1c14cd2884117f03bd26b56ff32d5575d92caa53c5391fa0e7e0ed4f3c815371",
+    "gate_spec_sha256": "0bafcc1cac9f1666b8bb4b1dfb3e17341bcd6562da2fa732e48af6d11f4c78b3",
+    "input_manifest_raw_sha256": "3b13488716a366676813bff567da91f216a426c94bd1fe43c22824f73b26d521",
+    "control_method_raw_sha256": "02a94b07a19901ec41e9e26c25ce156b80c0cf67b35a17f00cf8ca6087699971",
+    "v2_registry_raw_sha256": "8356cfb9311f34738f9de4f10e8189d39a43a38fbc97b34a9d4ad3e9bd243101"
+  },
+  "no_p_q_fdr": true,
+  "no_categorical_cell_labels": true,
+  "records": [
+    {
+      "program_id": "cd4_ctl_like",
+      "condition": "Rest",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "cd4_ctl_like|Rest",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.746295621111058,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": "PRF1",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "cd4_ctl_like|Rest",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 0.5830042037059001,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": "PRF1",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "cd4_ctl_like",
+      "condition": "Stim48hr",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "cd4_ctl_like|Stim48hr",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 0.6031074258461223,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": "GZMB",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "cd4_ctl_like",
+      "condition": "Stim8hr",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "cd4_ctl_like|Stim8hr",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 1.1899237314433537,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D3",
+          "worst_marker": "GZMB",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "diff_activated",
+      "condition": "Rest",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Rest",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.5535946811144762,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": "MKI67",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Rest",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 0.3291238704855382,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D3",
+          "worst_marker": "MKI67",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "diff_activated",
+      "condition": "Stim48hr",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Stim48hr",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.774328501712848,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": "MKI67",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Stim48hr",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 1.3608138676217634,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "IL2RA",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "diff_activated",
+      "condition": "Stim8hr",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Stim8hr",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.75070019925904,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "TNFRSF9",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_activated|Stim8hr",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 1.126320666743067,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "IL2RA",
+          "worst_seed": null
+        }
+      ]
+    },
+    {
+      "program_id": "diff_checkpoint",
+      "condition": "Rest",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_checkpoint|Rest",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.3107622093439082,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "HAVCR2",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_checkpoint|Rest",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 0.3977691755427863,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "HAVCR2",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "control_draw_sensitivity",
+          "stratum_instance": "diff_checkpoint|Rest",
+          "metric": "spearman_rho(score_primary, score_alt_seed)",
+          "observed_value": 0.8370836467504307,
+          "operator": ">=",
+          "threshold": 0.9,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D2",
+          "worst_marker": null,
+          "worst_seed": 12359
+        }
+      ]
+    },
+    {
+      "program_id": "diff_checkpoint",
+      "condition": "Stim48hr",
+      "production_selectable": false,
+      "raw_stage1_selectable": false,
+      "failed_or_undefined_hard_gates": [
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "diff_checkpoint|Stim48hr",
+          "metric": "spearman_rho(panel_mean_full, panel_mean_minus_gene)",
+          "observed_value": 0.7770820733041807,
+          "operator": ">=",
+          "threshold": 0.8,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D3",
+          "worst_marker": "LAG3",
+          "worst_seed": null
+        },
+        {
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+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "TNFRSF18",
+          "worst_seed": null
+        },
+        {
+          "gate_id": "lomo_panel_robustness",
+          "stratum_instance": "treg_like|Stim8hr",
+          "metric": "median(abs(delta_panel))/iqr(panel_mean_full)",
+          "observed_value": 0.5229826788038445,
+          "operator": "<=",
+          "threshold": 0.25,
+          "result": "fail",
+          "metric_defined": true,
+          "undefined_reason": null,
+          "consequence": "program_condition_nonselectable",
+          "worst_donor": "D1",
+          "worst_marker": "TNFRSF18",
+          "worst_seed": null
+        }
+      ]
+    }
+  ],
+  "self_canonical_sha256": "eb18d499037a7f2e18198f29393bcf8f7d15e4a1e13bffda8342a1c4e7c37253"
+}

stage1-continuous-v3.0.1/validation/stage01_validation_independent_check.json

@@ -0,0 +1,49 @@
+{
+  "schema": "spot.stage01_validation_independent_check.v1",
+  "method_version": "stage1-continuous-v3.0.1",
+  "purpose": "Generator != verifier record for the T7b validation artifact. Provenance only: it records that the lead independently observed the artifact's integrity + representative gates. It contains NO gate reinterpretation and NO T8/selectability decision. It contains no host name, user name, absolute/home path, session/frame id, or workspace locator.",
+  "artifact_verified": {
+    "repo_path": "01_programs/app/data/stage01_validation.json",
+    "raw_sha256": "1c14cd2884117f03bd26b56ff32d5575d92caa53c5391fa0e7e0ed4f3c815371",
+    "byte_identical_across_all_lead_verified_copies": true,
+    "byte_identical_note": "verified identical by raw SHA-256 across every copy the lead inspected; the copy locations are internal and intentionally omitted from this release artifact.",
+    "artifact_self_hash_validation_canonical_sha256": "c849dd7caf58a6735812e18399404ae01cbb40a5d73c2efdb9182b7f4278f173",
+    "identity_note": "raw file SHA-256 is authoritative; the artifact's self-declared canonical hash is carried but not independently reproduced (its canonicalization recipe was not re-derived), consistent with pre-flight rule 2."
+  },
+  "hash_bundle_reconciliation": {
+    "reconciled_against": "committed frozen Stage-1 v3 artifacts (repo)",
+    "gate_spec_sha256": {"embedded": "0bafcc1cac9f1666b8bb4b1dfb3e17341bcd6562da2fa732e48af6d11f4c78b3", "committed_file_raw_sha256": "0bafcc1cac9f1666b8bb4b1dfb3e17341bcd6562da2fa732e48af6d11f4c78b3", "match": true},
+    "bins_v3_csv_raw_sha256": {"embedded": "5cf42fcdd6db26119ebde96f172dae12c8d5fe34b1202e34db1b586478a96fd8", "committed_file_raw_sha256": "5cf42fcdd6db26119ebde96f172dae12c8d5fe34b1202e34db1b586478a96fd8", "match": true},
+    "bins_v3_content_sha256": {"embedded": "32f926cace9322752aba10557b1bafe3e0c8f9d8f285551fcd2d3648bd335f78", "matches_committed": true},
+    "controls_v3_csv_raw_sha256": {"committed_file_raw_sha256": "79764283a3429a103ed87a41b88a0c094fac84a7f46eebcb034d156e8573de75", "provenance": "artifact loaded controls from the committed controls_v3.csv; confirmed by artifact integrity primary_redraw_matches_committed=true"},
+    "input_h5ad_raw_sha256": {"embedded": "2edc6d318415c8b0ee779d707ab86e26ddb6f0274db51ab4a12f21ebfda50e43", "matches_committed": true, "authoritative_identity": true},
+    "input_h5ad_canonical_sha256": {"value": "4ba50ccdf759115297b92bdfb7ad65c5c952b84093314245d21fe9af19d0f714", "status": "ARCHIVED Phase-1 diagnostic (not a current verified hash)"},
+    "scores_canonical_content_sha256": "43c4296d5166740c334441a69df23bb440a073382bbe79628a3bb89e43d51316",
+    "coef_matrix_sha256": "ed1e26da9f255fdcddf56c5f4de113bb41147e34221a4faac35d79bf665c6e8c"
+  },
+  "independent_recomputations": {
+    "reproducibility_status": "independently_observed_not_reproducible_from_release",
+    "reproducibility_note": "These checks were computed independently by the lead this session but are NOT reproducible from the committed release artifacts alone: they require the pinned input h5ad (raw SHA-256 in inputs_by_hash.h5ad_raw_sha256; fetchable at the pinned HF revision e5fcf98b56a9302921d402e97fc5a190bd88f9a6), a numpy/scipy/pandas/h5py/pyarrow environment, and non-trivial compute. The independent verifier code is NOT committed. This record therefore asserts INDEPENDENT OBSERVATION, not a from-release reproducibility guarantee.",
+    "environment_identity": {"python": "3.11.15", "numpy": "2.4.6", "scipy": "1.17.1", "pandas": "2.3.3", "h5py": "3.16.0", "pyarrow": "24.0.0", "captured_from": "the conda interpreter that actually ran the independent scripts this session"},
+    "inputs_by_hash": {"h5ad_raw_sha256": "2edc6d318415c8b0ee779d707ab86e26ddb6f0274db51ab4a12f21ebfda50e43", "bins_raw_sha256": "5cf42fcdd6db26119ebde96f172dae12c8d5fe34b1202e34db1b586478a96fd8", "controls_raw_sha256": "79764283a3429a103ed87a41b88a0c094fac84a7f46eebcb034d156e8573de75", "gate_spec_raw_sha256": "0bafcc1cac9f1666b8bb4b1dfb3e17341bcd6562da2fa732e48af6d11f4c78b3", "scores_canonical_content_sha256": "43c4296d5166740c334441a69df23bb440a073382bbe79628a3bb89e43d51316"},
+    "sample_determinism": {"rule": "score sample = np.unique(np.linspace(0, n_cells-1, 250).astype(int)) over the parquet in h5ad row order; overlay check = first 2000 overlay cells x 3 score columns; both FULLY DETERMINISTIC with NO RNG seed", "rng_seed": "not_applicable_deterministic_linspace", "sampled_barcode_set_sha256": "not_pinned_in_release", "sampled_barcode_set_note": "the exact sampled-barcode-set hash requires the pinned h5ad/parquet (raw_sha256 in inputs_by_hash), which are not committed to the release; the independent claim is therefore kept limited to the recomputed value counts stated per check and is not broadened to the full population"},
+    "checks": [
+      {"name": "controls_reconstruct", "provenance": "LEAD independent recompute", "method_semantics": "recompute per-gene mean of the pinned pre-normalized/log1p .X matrix (author-provided median-total-normalized ~9819 + log1p; no raw-counts layer) via chunked float64 CSR column-sum over all 396k -> divN bins -> detected-minus-marker eligible pool -> keyed SHA-256 draws; compare to committed controls", "denominator": "2100 control rows across 11 primary programs + activation_predictor", "observed": "byte-identical (0 mismatches on program_id,bin,rank)"},
+      {"name": "bins_acceptance", "provenance": "LEAD independent recompute", "method_semantics": "load committed bins; compare marker-bin assignments and per-occupied-bin candidate_counts to the Phase-1 checkpoint; reconstruct all controls", "denominator": "53 marker genes; all occupied marker bins; 2100 controls", "observed": "marker_bins 0 mismatches; occupied-bin candidate_counts 0 mismatches; 2100 controls reconstruct"},
+      {"name": "scores_generator_integrity_artifact_reported", "provenance": "GENERATOR self-check reported by the artifact (field integrity.primary_score_exact_equal_after_5dp_round in stage01_validation.json); NOT an independent lead computation", "denominator": "396000 cells x 11 programs = 4356000 values", "observed": "4356000/4356000 exact after canonical 5dp rounding"},
+      {"name": "scores_lead_independent_sample", "provenance": "LEAD independent recompute from the pinned pre-normalized/log1p .X matrix (author-provided median-total-normalized ~9819 + log1p; no raw-counts layer) + committed controls (distinct from and much smaller than the generator check above)", "denominator": "250 unique cells x 11 programs = 2750 score values, plus 250 activation-adjusted residuals, plus 6000 overlay-vs-full value comparisons over 40000 overlay cells", "observed": "sampled scores max abs err vs emitted = 4.999999999949489e-06 (<= 5e-6 inclusive; consistent with exact-after-5dp because scores are stored at 5dp); actadj sample max abs err 4.999999999949489e-06; overlay==full max abs err 0.0; one summary median matched", "claim_scope": "this independent result claims ONLY the 2750 sampled score values (+250 actadj, +6000 overlay comparisons) it actually recomputed, NOT the full 4356000-value population"},
+      {"name": "gate_lomo_failing", "provenance": "LEAD independent recompute", "method_semantics": "cell-level LOMO (Spearman of panel_mean_full vs panel_mean_minus_gene, average ranks no p-value; median|delta|/IQR) per donor at a condition; report worst over markers x donors", "denominator": "th1_like (4 markers) and cd4_ctl_like (6 markers), each x 4 donors, at condition Rest", "observed": "th1_like|Rest worst rho=0.764173 (D1), ratio=0.584872, matching the artifact values 0.7641729607325386 and 0.5848723435562414 to 6 dp; cd4_ctl_like|Rest also FAIL independently"},
+      {"name": "gate_passing_and_advisory", "provenance": "LEAD independent recompute", "method_semantics": "condition_measurability (score IQR>0 and >=2 panel genes detected in >=1% cells per donor); pair_redundancy (|Spearman(A,B)|>=0.90 in >=3/4 donors)", "denominator": "cd4_ctl_like|Rest x 4 donors; th1_like~treg_like|Rest x 4 donors", "observed": "condition_measurability cd4_ctl_like|Rest PASS; pair_redundancy th1_like~treg_like|Rest |rho|>=0.90 in 0/4 -> not redundant (matches artifact)"}
+    ],
+    "follow_up_proposal": "To upgrade these to reproducible-from-pinned-input, commit a single clean, path-parameterized, no-leak verifier under 01_programs/analysis/ (inputs by argument, not hardcoded), record its code SHA-256 + exact environment lock + the input hashes above, as a separately reviewed step. Not done in this preservation commit."
+  },
+  "t7b_outcome_recorded_as_is": {
+    "stage1_selectable_by_condition": "0 of 33 (every program x condition fails the pre-registered cell-level LOMO gate)",
+    "stage2_base_portability": "10/11 pass; th9_like fails (0 panel genes in effect universe)",
+    "advisory_flags": "empty (pair/off-axis/donor)",
+    "overlay_release": "not_ok (1 overlay_distributions failure; blocks overlay release only, separate from selectability)",
+    "cp10k_v2_comparison": "undefined/descriptive",
+    "note": "This is the honest result of the pre-registered gate AS WRITTEN. No panel/threshold/control/seed retuning was performed. Any reclassification or additional test is a separate proposal and is NOT applied here."
+  },
+  "no_reinterpretation_assertion": "This record and the accompanying validation artifact preserve the pre-registered gate's output verbatim. No gate reinterpretation, no T8 decision, no manufactured selectable pair."
+}