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VCDesign

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Boom5426 commited on 16 days ago

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f6bed3b

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1 Parent(s): 21ccdaf

Add manifests, evaluation records, and external baseline scores

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Files changed (27) hide show

DATA_MANIFEST.json +336 -0
README.md +58 -0
inputs/cache_manifest.json +20 -0
inputs/candidate_knowledge_freeze.json +41 -0
inputs/external_baselines/scores/HepG2.npz +3 -0
inputs/external_baselines/scores/Jurkat.npz +3 -0
inputs/external_baselines/scores/RPE1.npz +3 -0
inputs/freeze.json +0 -0
inputs/gene_order.txt +8248 -0
inputs/mapkg_manifest.json +94 -0
inputs/source_goal_manifest.json +82 -0
inputs/source_goal_row_metadata.parquet +3 -0
records/external_baselines/MANIFEST.json +1385 -0
records/external_baselines/VERIFICATION.json +60 -0
records/external_baselines/external_baselines_v1.json +0 -0
records/final_clean/VCDesign_FINAL_LOCK.json +364 -0
records/final_clean/locked_evaluation.json +1179 -0
records/final_clean/selection.json +1429 -0
records/final_clean/train_manifest.json +318 -0
records/four_context/HepG2_build_manifest.json +75 -0
records/four_context/HepG2_verification.json +7 -0
records/four_context/Jurkat_build_manifest.json +75 -0
records/four_context/Jurkat_verification.json +7 -0
records/four_context/K562_verification.json +7 -0
records/four_context/RPE1_build_manifest.json +59 -0
records/four_context/RPE1_verification.json +7 -0
records/source_goal/pairing_semantics_audit.json +181 -0

DATA_MANIFEST.json ADDED Viewed

	@@ -0,0 +1,336 @@

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+  "source_run_manifest_schema": "VCDESIGN_CED_FROZEN_INPUT_INDEX_V1"
+}

README.md ADDED Viewed

	@@ -0,0 +1,58 @@

+---
+pretty_name: VCDesign-CED processed inputs and frozen evaluation artifacts
+tags:
+- single-cell
+- perturb-seq
+- intervention-design
+---
+# VCDesign-CED processed data
+This repository stores the frozen processed inputs used by the VCDesign-CED
+paper, plus the selected base-model checkpoint and compact evaluation records.
+The source single-cell H5AD files are obtained from the original public
+releases and are not duplicated here.
+## Contents
+| Directory | Contents |
+|---|---|
+| `inputs/` | The 19 frozen inputs referenced by the paper's training configuration, plus source-goal metadata |
+| `inputs/four_context/packs/` | K562, RPE1, HepG2 and Jurkat processed context packs |
+| `inputs/external_baselines/scores/` | Frozen external-comparator score matrices for RPE1, HepG2 and Jurkat |
+| `checkpoints/` | Selected epoch-8 VCDesign-CED base-model checkpoint |
+| `records/` | Training, selection, evaluation, context-build and comparator verification records |
+| `DATA_MANIFEST.json` | File sizes, release SHA-256 values and original SHA-256 values where a record was anonymized |
+`DATA_MANIFEST.json` identifies the exact bytes uploaded. JSON records that
+contained compute-host paths have only those path strings replaced with release
+relative paths or `UNBUNDLED/<filename>` labels. The original file hash is
+retained beside each transformed record's release hash. Numeric arrays and model
+weights are copied byte-for-byte and checked against the frozen run manifest.
+The processed data correspond to the code package's
+`configs/asset_config.example.json` path layout. To place only the data files in
+a checkout of that package without replacing its README:
+```bash
+hf download Boom5426/VCDesign --repo-type dataset \
+  --include 'inputs/**' 'checkpoints/**' 'records/**' 'DATA_MANIFEST.json' \
+  --local-dir /path/to/code-package
+python3 tools/verify_processed_data.py --root /path/to/code-package
+```
+The exact repository revision should be pinned for a reproduction run. The
+selected checkpoint was epoch 8, with frozen SHA-256
+`58da13d252faf9bcaa74c53345c0afc380882bdd5f410a77cfa5044f9a6e9484`.
+## Original public sources
+- [Replogle et al. K562 genome-scale and RPE1 Perturb-seq](https://plus.figshare.com/articles/dataset/_Mapping_information-rich_genotype-phenotype_landscapes_with_genome-scale_Perturb-seq_Replogle_et_al_2022_processed_Perturb-seq_datasets/20029387)
+- [GEO GSE264667 HepG2 and Jurkat screens](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264667)
+- [STRING v12.0 physical interaction data](https://version-12-0.string-db.org/cgi/download)
+- [MAP and MAP-KG](https://github.com/MAGIC-AI4Med/MAP)
+- [ESM-2](https://github.com/facebookresearch/esm)
+The derived files are tied to those source versions; the K562 genome-scale
+screen is distinct from the K562 essential screen. Cite the original data and
+knowledge resources when using this collection.

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+{
+  "all_models_must_use_this_cache": true,
+  "cache_file": "inputs/responses_ab.npy",
+  "cache_ids_file": "inputs/eligible_ids.npy",
+  "cache_ids_sha256": "40e104ed924c109d621f15bc5bb3bf899ca89c3f14db046b5aa5ae0c4ce611a7",
+  "cache_sha256": "bb48bae7f864c66b242a77cef064ff967b418d22bb11416630548f6a6d094a94",
+  "cache_shape": [
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+    9205,
+    8248
+  ],
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+  "identity_count": 9205,
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+  "metadata_sha256": "17e5340e590b7e72cf2ab36fc75f6cccb55de89dfd38932121f0a385989faee1",
+  "response_recipe": "M3 locked A/B control-corrected pseudobulk response",
+  "schema": "VCDesign_V2_REPLOGLE_RESPONSE_CACHE_V1",
+  "source_sha256": "d3269d9c863d96555eba768b42ab330cc1b57493cd33b4ac8fe7fbab8278f104",
+  "status": "FROZEN_SHARED_RESPONSE_CACHE"
+}

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+    "lock.py": "34771ddd73667516629c6f048d209d991b446eaacf3faa996e9deb14a042918f",
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+    "test_protocol.py": "1af36605d8106667f9339477c81e219e1952756a32560dd1a46defaec41e8217"
+  },
+  "created": "2026-09-11T20:24:03+0800",
+  "environment": {
+    "device": "NVIDIA GeForce RTX 4090",
+    "numpy": "2.2.6",
+    "python": "3.11.14",
+    "scikit_learn": "1.7.2",
+    "scipy": "1.14.1",
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+  },
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+  "sha256": {
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+  },
+  "status": "FROZEN_BEFORE_RESPONSE_OR_G_SELECT_READ"
+}

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inputs/mapkg_manifest.json ADDED Viewed

	@@ -0,0 +1,94 @@

+{
+  "asset": {
+    "path": "inputs/mapkg_features.npz",
+    "sha256": "0fb285e600410001a31a20056b4d4ad39a43f9c17aa4f2dcfc35f61f261aff5e"
+  },
+  "checkpoint": {
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+    "path": "UNBUNDLED/mapkg_encoder_v3.pt",
+    "sha256": "118d14ea3756a63d39044660254951a18340f59b136c391ae3f2578f6d19219b",
+    "size": 1126763160,
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+    "state_keys_sha256": "4a871cc2c7bb16aca5e337ae85ee474f76e71310d7168cddffda7e5861220633",
+    "training_meta": {
+      "epoch": 159,
+      "loss": 0.40466785430908203,
+      "step": 130539
+    }
+  },
+  "coverage": {
+    "MAPKG": {
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+        "total": 1000
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+      "KG_fit": {
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+      "KG_select": {
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+      "universe": {
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+        "total": 17775
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+    },
+    "STRING": {
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+        "present": 957,
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+      "universe": {
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+    }
+  },
+  "created": "2026-09-11T21:51:31+0800",
+  "details": {
+    "MAPKG": {
+      "definition": "frozen checkpoint gene_projector applied to released ESM2 gene embedding; no response fine-tuning",
+      "dimension": 1024,
+      "nondegenerate": 1024
+    },
+    "STRING": {
+      "dimension": 512,
+      "nondegenerate": 512
+    }
+  },
+  "governance": {
+    "MAPKG_finetuned": false,
+    "downstream_MAP_checkpoint_used": false,
+    "perturbation_response_read": false,
+    "relevance_read": false
+  },
+  "schema": "MAPKG_CANDIDATE_ADJUDICATION_V1_STATIC_FEATURES",
+  "sha256": {
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records/external_baselines/external_baselines_v1.json ADDED Viewed

The diff for this file is too large to render. See raw diff

records/final_clean/VCDesign_FINAL_LOCK.json ADDED Viewed

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records/final_clean/selection.json ADDED Viewed

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records/final_clean/train_manifest.json ADDED Viewed

	@@ -0,0 +1,318 @@

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+}

records/four_context/HepG2_build_manifest.json ADDED Viewed

	@@ -0,0 +1,75 @@

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+}

records/four_context/HepG2_verification.json ADDED Viewed

	@@ -0,0 +1,7 @@

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+}

records/four_context/Jurkat_build_manifest.json ADDED Viewed

	@@ -0,0 +1,75 @@

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+}

records/four_context/Jurkat_verification.json ADDED Viewed

	@@ -0,0 +1,7 @@

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+}

records/four_context/K562_verification.json ADDED Viewed

	@@ -0,0 +1,7 @@

+{
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+}

records/four_context/RPE1_build_manifest.json ADDED Viewed

	@@ -0,0 +1,59 @@

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+}

records/four_context/RPE1_verification.json ADDED Viewed

	@@ -0,0 +1,7 @@

+{
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+}

records/source_goal/pairing_semantics_audit.json ADDED Viewed

	@@ -0,0 +1,181 @@

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+    "path": "inputs/responses_ab.npy",
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+  "raw": {
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+}