Archive FastPLMs validation evidence and golden tensors

Move the reviewed public PR49 evidence payloads to a checksummed dataset. Historical v2 confidence metrics remain marked as requiring recomputation. No confidence checkpoint weights are included.

README.md

@@ -0,0 +1,23 @@
+---
+pretty_name: FastPLMs research and validation artifacts
+license: other
+license_name: source-specific-terms
+license_link: https://github.com/Synthyra/FastPLMs/blob/main/docs/licensing.md
+---
+# FastPLMs artifacts
+
+This dataset holds the measured reports and golden regression tensors maintained by [FastPLMs](https://github.com/Synthyra/FastPLMs). It is not a training dataset or a set of model checkpoints.
+
+The source repository keeps `evidence.toml`, which pins an immutable dataset revision and each payload's SHA-256 digest and size. Fetch explicitly with `python -m tools.artifacts.evidence_store fetch` before offline documentation, release, or parity checks.
+
+Paths preserve the source workspace layout: `docs/evidence`, `docs/validation`, and `tests/goldens`. Runtime configuration, model manifests, dependency locks, and small synthetic fixtures remain in Git.
+
+## Evidence status
+
+The v2 confidence reports preserve historical numeric results. Their `metrics_review` fields mark correlations, bootstrap intervals, and acceptance gates as requiring recomputation after the tied-rank correction. Raw per-target predictions were not recovered from the closed training workstation or W&B. These archived values must not be presented as corrected evaluation results. No v2 confidence weights are included.
+
+Other artifacts retain their recorded source revisions, environments, and evidence boundaries. Presence in this dataset is not an assertion that all release gates pass.
+
+## Terms and provenance
+
+Payloads originated in the public FastPLMs repository at PR #49 (`1ae17f2b3955db28fe9c076b5c7e2394c6fc83ac`), with review-status annotations added to the v2 confidence reports. Golden metadata identifies originating checkpoints and source revisions. Applicable model and source terms remain in effect; migration does not relicense them. Consult the source repository's `LICENSES`, model manifest, and licensing documentation. No blanket permissive license is asserted for the combined collection.

docs/evidence/attention/backend_latency.json

@@ -0,0 +1,203 @@
+{
+  "schema_version": 1,
+  "method": "Randomly initialized models at published dimensions, FP32 parameters under CUDA BF16 autocast, inference mode. Each backend runs in its own process, three interleaved rounds per case; a round reports the median forward latency after warm-up. One batch is 8 rows of 512 positions.",
+  "residues_per_batch": {
+    "padded": 2336,
+    "full": 4096
+  },
+  "limitations": "Descriptive latency of an uncommitted working tree on cloud workers. It orders backends for automatic selection and is not a release benchmark or a parity claim.",
+  "runs": [
+    {
+      "run": "20260921T131922-backend-bench-b42b0fec",
+      "source": {
+        "revision": "d9a23718713905dd907add3d7b7a85d6e8e49f23",
+        "dirty": true,
+        "changed_paths": 104
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+      "environment": {
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+        "platform": "Linux-4.19.0-gvisor-x86_64-with-glibc2.36",
+        "torch": "2.13.0+cu130",
+        "transformers": "5.13.0",
+        "cuda": "13.0",
+        "gpu": "NVIDIA L4",
+        "compute_capability": [
+          8,
+          9
+        ]
+      },
+      "cases": {
+        "dplm-full": {
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+            "flash_attention_3": 79.99282836914062
+          },
+          "speedup_over_sdpa": {
+            "sdpa": 1.0,
+            "flash_attention_3": 0.9940602699903289
+          },
+          "failures": {}
+        },
+        "dplm-padded": {
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+            "flash_attention_3": 74.23538970947266
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+          "speedup_over_sdpa": {
+            "sdpa": 1.0,
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+          "failures": {}
+        },
+        "esm2-full": {
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+            "flash_attention_2": 75.3699836730957,
+            "flash_attention_3": 78.59302520751953
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+          "failures": {}
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+        "esm2-padded": {
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+          "failures": {}
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+        "esmpp-full": {
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+          "failures": {}
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+        "esmpp-padded": {
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+          "failures": {}
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+      }
+    },
+    {
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+      "environment": {
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+        "torch": "2.13.0+cu130",
+        "transformers": "5.13.0",
+        "cuda": "13.0",
+        "gpu": "NVIDIA H100 80GB HBM3",
+        "compute_capability": [
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+          0
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+      },
+      "cases": {
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+          "failures": {}
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+          "failures": {}
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+        "esm2-full": {
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+            "flash_attention_3": 30.517087936401367
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+          "speedup_over_sdpa": {
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+            "flash_attention_2": 0.8303694056424473,
+            "flash_attention_3": 0.7399599793571684
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+          "failures": {}
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+        "esm2-padded": {
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+          "speedup_over_sdpa": {
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+          "failures": {}
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+        "esmpp-full": {
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+          "speedup_over_sdpa": {
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+            "flash_attention_3": 0.7233691312584395
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+          "failures": {}
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+        "esmpp-padded": {
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+          "failures": {}
+        }
+      }
+    }
+  ]
+}

docs/evidence/confidence/esmfold2_300-package.json

@@ -0,0 +1,192 @@
+{
+  "status": "passed",
+  "model_id": "esmfold2_300",
+  "artifact": "/vol/confidence/esmfold2_300/package/artifact",
+  "base_repo": "Synthyra/ESMFold2-300",
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+      "rcsb_multimer_val": {
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+    "gpu": "NVIDIA H100 80GB HBM3",
+    "backbone_precision": "bf16",
+    "head_parameters": "float32",
+    "deterministic_algorithms": true,
+    "estimated_dollars_per_second": 0.0012204400000000002,
+    "maximum_seconds": 36000,
+    "selection": "both_heads_improve_with_rank_guard"
+  },
+  "complete_artifact_compliance": false,
+  "inference": {
+    "coordinate_equality": true,
+    "samples": [
+      1,
+      2
+    ],
+    "seed": 17,
+    "loops": 3,
+    "diffusion_steps": 15,
+    "dtype": "fp32 parameters, bf16 autocast",
+    "backend": "sdpa",
+    "confidence_shapes": {
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+          896
+        ],
+        "plddt": [
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+        "pae": [
+          1,
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+        "ptm": [
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+        "iptm": [
+          1
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+      },
+      "2": {
+        "plddt_per_atom": [
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+        "plddt": [
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+        "ptm": [
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+        "iptm": [
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+      }
+    },
+    "cif_atom_count": 870,
+    "cif_chain_ids": [
+      "A",
+      "B"
+    ],
+    "peak_memory_bytes": 1818710528,
+    "gpu": "NVIDIA H100 80GB HBM3",
+    "torch_version": "2.13.0+cu130"
+  },
+  "elapsed_seconds": 47.663520231,
+  "controller_app_id": "ap-AbpkD7NbtLPFrbEex1ucXR",
+  "controller_call_id": "568712ef0c9e4737a8b86fad96129b59"
+}

docs/evidence/confidence/esmfold2_300-v2.json

@@ -0,0 +1,1169 @@
+{
+  "status": "complete",
+  "campaign": "confidence-v2",
+  "metrics_review": {
+    "status": "requires_recomputation",
+    "reason": "The original Spearman implementation assigned distinct ranks to tied values. Correlations, bootstrap intervals, and acceptance gates must be recomputed with average tied ranks.",
+    "historical_values_preserved": true,
+    "raw_prediction_recovery": {
+      "status": "unavailable",
+      "details": "The GH200 workstation is closed. W&B contains no logged artifacts or raw per-target prediction records for either v2 run; aggregate history cannot reconstruct corrected metrics.",
+      "required_files": [
+        "~/data/confidence-v2/evaluation/esmfold2_300/records.json",
+        "~/data/confidence-v2/evaluation/esmfold2/records.json"
+      ]
+    },
+    "training_history_audit": {
+      "wandb_url": "https://wandb.ai/lhallee/fastplms-confidence/runs/d5587e06871a",
+      "history_rows": 780,
+      "metric": "train/skipped_targets",
+      "maximum": 0,
+      "scope": "All 780 update rows were inspected.",
+      "conclusion": "The skipped-target gradient bug did not affect this recorded training run because no training target was skipped."
+    }
+  },
+  "model_id": "esmfold2_300",
+  "data": {
+    "dataset": "Synthyra/AtlasFold-Data",
+    "configurations": [
+      "rcsb",
+      "rcsb_multimer"
+    ],
+    "maximum_resolution_angstrom": 4.0
+  },
+  "training": {
+    "donor_repo": "biohub/ESMFold2-Experimental-Fast-Cutoff2025",
+    "donor_revision": "74b88548bf19688b8727432db0d698cb2e1d8783",
+    "donor_weight_sha256": "4e903b740ad6ad704ec60881bfd593e0d6c874a630ffa0f0838276e0b665088f",
+    "wandb_url": "https://wandb.ai/lhallee/fastplms-confidence/runs/d5587e06871a",
+    "updates": 780,
+    "stopped_by": "planned_updates",
+    "elapsed_hours": 19.363341560259997,
+    "selected_checkpoint": "final-ema.safetensors",
+    "final_validation": {
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+      "within_target_plddt_accuracy": 0.5428571428571428,
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+      "within_target_iptm_pairs": 383.0,
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+    "config": {
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+      "targets_per_update": 16,
+      "learning_rate": 0.0001,
+      "minimum_learning_rate": 1e-05,
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+      "maximum_seconds": 73800,
+      "validation_limit": null,
+      "num_loops": 3,
+      "num_sampling_steps": 50,
+      "seed": 17
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+  },
+  "splits": {
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+}

docs/evidence/confidence/esmfold2_300.json

@@ -0,0 +1,387 @@
+{
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docs/evidence/confidence/esmfold2_600-package.json

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docs/evidence/confidence/esmfold2_600-v2.json

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docs/evidence/confidence/esmfold2_600.json

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docs/evidence/esmfold2/folding_cost.json

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docs/validation/esmfold2_300_artifact_reload.json

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docs/validation/esmfold2_300_backbone.json

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docs/validation/esmfold2_300_published_loading.json

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docs/validation/esmfold2_300_quickstart.json

@@ -0,0 +1,34 @@
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docs/validation/esmfold2_600_backbone.json

@@ -0,0 +1 @@
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docs/validation/esmfold2_small_300_candidate_metadata.json

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docs/validation/esmfold2_small_300_comparison.json

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docs/validation/esmfold2_small_300_reference_metadata.json

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docs/validation/esmfold2_small_dependencies.json

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+}

tests/goldens/ankh2_large.json

@@ -0,0 +1,88 @@
+{
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+    "-m",
+    "tools.goldens",
+    "--native-root",
+    "artifacts/reference",
+    "--output-root",
+    "tests/goldens",
+    "--model",
+    "ankh2_large"
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+      "revision": "02b4e25ce5389b9e771c9df6e546c62af1216f8e",
+      "url": "https://github.com/agemagician/Ankh.git"
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