Update collection and curation progress 2026-10-13T18:44:23+00:00

ATTRIBUTION.md

@@ -21,3 +21,5 @@
 
 The repository uses source-specific data licenses. Dataset preparation does not
 transfer authorship of the original structures or predictions.
+
+- AFDB bulk mirror: [timodonnell/afdb-1.6M](https://huggingface.co/datasets/timodonnell/afdb-1.6M), derived from AFDB-24M, pinned revision `a7ededeb7caeaef3892f40f2e4df3bb9236b02f8`. Source coordinates are AFDB v4, CC BY 4.0; source structural cluster labels originate from the Steinegger lab AFDB clustering.

README.md

@@ -14,31 +14,37 @@ pretty_name: SimpleFoldData
 
 # SimpleFoldData
 
-An independently prepared, versioned protein-structure dataset based on the
-public target lists used by Apple's SimpleFold. The intended first release is
-**1,000,000 distinct protein sequences with validated structures**, combining
-PDB, author-listed AFDB SwissProt, and cluster-balanced AFESM representatives.
+An independently curated protein-structure dataset. The primary pool now combines
+**[AFDB-1.6M](https://huggingface.co/datasets/timodonnell/afdb-1.6M)** with experimental
+PDB chains initially released before 2020-05-01. The target is **1,000,000 distinct
+sequences with verified coordinates**, preferring PDB for exact duplicates.
 
-**Status: build in progress. No training-ready release has been declared.**
-The initial catalog records published IDs and structural-cluster membership.
-Catalog membership does not imply that a sequence has been recovered, a
-structure verified, or benchmark homology exclusions completed.
+**Status: build in progress.** AFDB bulk download and validation are running.
+Final selection, coordinate packing, and public upload are queued after both
+source collection jobs succeed. ESM-C 6B production embeddings are not yet queued.
 
 ## Selection and verification
 
-The build retains Apple's full source inventory and a deterministic seed-17
-cluster ordering. It will deduplicate exact sequences while keeping all source
-aliases, source versions, structure hashes, and historical cluster assignments.
-PDB candidates use an initial-release cutoff before 2020-05-01. SwissProt
-confidence filters are mean pLDDT >85 and population standard deviation <15;
-AFESM confidence must exceed 80 on the 0–100 scale. No 256/1024-residue admission
-cap is imposed. Missing identities, changed versions, inaccessible structures,
-and unresolved fragments remain explicit in audit ledgers.
+AFDB source revision: `a7ededeb7caeaef3892f40f2e4df3bb9236b02f8`.
+The source selects one representative per AFDB v4 structural cluster, with an
+upstream sequence-length limit of 2,048 residues. It is not Apple's exact AFESM
+selection. Original source cluster and sequence-cluster labels are retained;
+no joint structural reclustering of PDB and AFDB is claimed.
 
-Author lists refer to historical predictions. Retrieved modern payloads are
-identified by their actual source version and hash; they are not represented
-as original historical bytes. Structural-cluster labels initially reproduce
-the author's membership, not a newly recomputed clustering of changed models.
+Every downloaded Parquet file is checked against its source SHA-256. Prediction
+records must have canonical sequences, complete N/CA/C backbones, finite atom
+coordinates, sequence/coordinate identity, and recomputed mean pLDDT >80.
+Experimental PDB chains retain full entity sequences and missing-residue indices;
+at least 80% of residues must have observed N/CA/C backbone atoms.
+
+The final pool includes eligible unique PDB sequences first, then fills to the
+target with AFDB records in deterministic seed-17 sequence-hash order. It is sorted
+by sequence length and hash. Aliases are retained separately. Final selected
+coordinate bytes are rechecked against their recorded SHA-256 before packing.
+
+Earlier Apple source catalogs, SwissProt candidates and AFESM work are preserved
+as supplementary sources, outside this primary AFDB/PDB selection. Existing files
+under `swissprot/` are not the final selected release.
 
 The final source-pool selection must pass sequence/coordinate identity checks,
 exact deduplication, and count reconciliation. This is a general-purpose data
@@ -60,6 +66,6 @@ receive an explicit embedding status; they are never silently cropped.
 
 ## Live progress
 
-Updated 2026-10-13T18:24:47+00:00. Coordinate-qualified candidates before deduplication: **275,530**. Final selected unique sequences: **not yet measured**.
+Updated 2026-10-13T18:44:23+00:00. Coordinate-qualified candidates before deduplication: **157,837**. Final selected unique sequences: **not yet measured**.
 
 [Detailed progress and job status](reports/progress.md) · [Machine-readable status](reports/progress.json) · [HTML dashboard](reports/progress.html)

reports/progress.html

@@ -1,6 +1,6 @@
-<!doctype html><html><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta http-equiv="refresh" content="300"><title>SimpleFoldData progress</title><style>body{font:16px system-ui;background:#101922;color:#e6edf3;max-width:1050px;margin:40px auto;padding:24px}h1{font-size:38px}.grid{display:grid;grid-template-columns:repeat(auto-fit,minmax(240px,1fr));gap:14px}.card{background:#1c2b38;border:1px solid #355068;border-radius:12px;padding:20px}.card span{display:block;color:#b7cad8}.card strong{display:block;font-size:30px;margin-top:12px}pre{white-space:pre-wrap;background:#17232e;padding:20px;border-radius:12px}a{color:#8acfff}</style></head><body><h1>SimpleFoldData</h1><p>One million structures · collection and curation</p><p>Updated 2026-10-13T18:24:47+00:00</p><div class="grid"><div class="card"><span>Target distinct sequences</span><strong>1,000,000</strong></div><div class="card"><span>Author AFESM clusters indexed</span><strong>2,036,414</strong></div><div class="card"><span>Author AFESM-E membership rows indexed</span><strong>8,616,595</strong></div><div class="card"><span>Author SwissProt IDs indexed</span><strong>269,003</strong></div><div class="card"><span>Coordinate-qualified candidates (before global deduplication)</span><strong>275,530</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Structure candidates uploaded</span><strong>263,278</strong></div><div class="card"><span>Sequences embedded</span><strong>60</strong></div><div class="card"><span>Embedding bytes stored</span><strong>156,194,104</strong></div></div><h2>Build details</h2><pre># SimpleFoldData — collection and curation progress
+<!doctype html><html><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta http-equiv="refresh" content="300"><title>SimpleFoldData progress</title><style>body{font:16px system-ui;background:#101922;color:#e6edf3;max-width:1050px;margin:40px auto;padding:24px}h1{font-size:38px}.grid{display:grid;grid-template-columns:repeat(auto-fit,minmax(240px,1fr));gap:14px}.card{background:#1c2b38;border:1px solid #355068;border-radius:12px;padding:20px}.card span{display:block;color:#b7cad8}.card strong{display:block;font-size:30px;margin-top:12px}pre{white-space:pre-wrap;background:#17232e;padding:20px;border-radius:12px}a{color:#8acfff}</style></head><body><h1>SimpleFoldData</h1><p>One million structures · collection and curation</p><p>Updated 2026-10-13T18:44:23+00:00</p><div class="grid"><div class="card"><span>Target distinct sequences</span><strong>1,000,000</strong></div><div class="card"><span>Author AFESM clusters indexed</span><strong>2,036,414</strong></div><div class="card"><span>Author AFESM-E membership rows indexed</span><strong>8,616,595</strong></div><div class="card"><span>Author SwissProt IDs indexed</span><strong>269,003</strong></div><div class="card"><span>Coordinate-qualified candidates (before global deduplication)</span><strong>157,837</strong></div><div class="card"><span>Final selected unique sequences</span><strong>not yet measured</strong></div><div class="card"><span>Selected structures uploaded</span><strong>0</strong></div><div class="card"><span>Sequences embedded</span><strong>60</strong></div><div class="card"><span>Embedding bytes stored</span><strong>156,194,104</strong></div></div><h2>Build details</h2><pre># SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:24:47+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:44:23+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,9 +10,9 @@ Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 | Author AFESM clusters indexed | 2,036,414 |
 | Author AFESM-E membership rows indexed | 8,616,595 |
 | Author SwissProt IDs indexed | 269,003 |
-| Coordinate-qualified candidates (before global deduplication) | 275,530 |
+| Coordinate-qualified candidates (before global deduplication) | 157,837 |
 | Final selected unique sequences | not yet measured |
-| Structure candidates uploaded | 263,278 |
+| Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
 | Embedding bytes stored | 156,194,104 |
 
@@ -22,8 +22,9 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 
 - **Author inventory:** author_inventory_complete; swissprot_author_rows=269,003, afesm_author_rows=2,036,414, targets=2,305,417, clusters=2,036,414, memberships=8,616,595, afesm_representatives_unmapped=0, members_with_multiple_clusters=0
 - **SwissProt:** complete; coordinate_qualified=263,278, confidence_rejected=5,698, absent_from_available_archive=27
-- **AFESM:** running; coordinate_qualified=2,262, source_unavailable=205, confidence_rejected=17, validation_rejected=2
-- **PDB:** running; entry_processed=3,710, coordinate_qualified=9,990, validation_rejected=2
+- **AFESM (superseded):** superseded; coordinate_qualified=4,477, source_unavailable=403, confidence_rejected=46, validation_rejected=2
+- **AFDB bulk:** running; coordinate_qualified=131,065, validation_rejected=50,375
+- **PDB:** running; entry_processed=9,854, coordinate_qualified=26,772, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -55,12 +56,16 @@ JobID|State|Elapsed|ExitCode
 1320537|COMPLETED|00:02:11|0:0
 1320537.batch|COMPLETED|00:02:11|0:0
 1320537.extern|COMPLETED|00:02:11|0:0
-1320554|RUNNING|00:15:57|0:0
-1320554.batch|RUNNING|00:15:57|0:0
-1320554.extern|RUNNING|00:15:57|0:0
-1320625|RUNNING|00:11:30|0:0
-1320625.batch|RUNNING|00:11:30|0:0
-1320625.extern|RUNNING|00:11:30|0:0
+1320554|CANCELLED by 21014|00:31:03|0:0
+1320554.batch|CANCELLED|00:31:03|0:15
+1320554.extern|COMPLETED|00:31:03|0:0
+1320625|RUNNING|00:31:06|0:0
+1320625.batch|RUNNING|00:31:06|0:0
+1320625.extern|RUNNING|00:31:06|0:0
+1321100|RUNNING|00:04:39|0:0
+1321100.batch|RUNNING|00:04:39|0:0
+1321100.extern|RUNNING|00:04:39|0:0
+1321145|PENDING|00:00:00|0:0
 ```
 
 Next hourly update scheduled; remaining updates: 168.

reports/progress.json

@@ -1,5 +1,5 @@
 {
-  "updated_utc": "2026-10-13T18:24:47+00:00",
+  "updated_utc": "2026-10-13T18:44:23+00:00",
   "target": 1000000,
   "release_complete": false,
   "inventory": {
@@ -61,29 +61,50 @@
     "training_selection_complete": false
   },
   "afesm": {
-    "stage": "running",
+    "stage": "superseded",
     "counts": {
-      "coordinate_qualified": 2262,
-      "source_unavailable": 205,
-      "confidence_rejected": 17,
+      "coordinate_qualified": 4477,
+      "source_unavailable": 403,
+      "confidence_rejected": 46,
       "validation_rejected": 2
     },
-    "attempted": 2486,
-    "elapsed_seconds": 944.421954870224,
-    "processed_this_job": 2358,
+    "attempted": 4928,
+    "elapsed_seconds": 1851.2159233093262,
+    "processed_this_job": 4800,
     "candidate_limit": 850000,
     "workers": 4
   },
+  "afdb_bulk": {
+    "stage": "running",
+    "counts": {
+      "coordinate_qualified": 131065,
+      "validation_rejected": 50375
+    },
+    "shards_complete": 108,
+    "shards_total": 1000,
+    "rows_processed": 181440,
+    "bytes_complete": 7764109754,
+    "total_bytes": 71689983734,
+    "elapsed_seconds": 276.4593395907432,
+    "shards_this_job": 108,
+    "source_repository": "timodonnell/afdb-1.6M",
+    "source_revision": "a7ededeb7caeaef3892f40f2e4df3bb9236b02f8",
+    "workers": 4
+  },
   "pdb": {
     "stage": "running",
     "counts": {
-      "entry_processed": 3710,
-      "coordinate_qualified": 9990,
+      "entry_processed": 9854,
+      "coordinate_qualified": 26772,
       "validation_rejected": 2
     },
     "candidate_entry_limit": 163219,
-    "elapsed_seconds": 683.8736047744751
+    "elapsed_seconds": 1859.4233796596527
   },
+  "primary_sources": [
+    "afdb_bulk",
+    "pdb"
+  ],
   "curation": {},
   "upload": {
     "stage": "swissprot_candidates_uploaded",
@@ -237,6 +258,8 @@
     "encoder_stage": "1320495",
     "embedding_pilot": "1320498",
     "publish_sources": "1320537",
+    "afdb_bulk": "1321100",
+    "finalize_and_publish": "1321145",
     "hourly_progress": "1320419"
   },
   "scheduler": [
@@ -259,12 +282,16 @@
     "1320537|COMPLETED|00:02:11|0:0",
     "1320537.batch|COMPLETED|00:02:11|0:0",
     "1320537.extern|COMPLETED|00:02:11|0:0",
-    "1320554|RUNNING|00:15:57|0:0",
-    "1320554.batch|RUNNING|00:15:57|0:0",
-    "1320554.extern|RUNNING|00:15:57|0:0",
-    "1320625|RUNNING|00:11:30|0:0",
-    "1320625.batch|RUNNING|00:11:30|0:0",
-    "1320625.extern|RUNNING|00:11:30|0:0"
+    "1320554|CANCELLED by 21014|00:31:03|0:0",
+    "1320554.batch|CANCELLED|00:31:03|0:15",
+    "1320554.extern|COMPLETED|00:31:03|0:0",
+    "1320625|RUNNING|00:31:06|0:0",
+    "1320625.batch|RUNNING|00:31:06|0:0",
+    "1320625.extern|RUNNING|00:31:06|0:0",
+    "1321100|RUNNING|00:04:39|0:0",
+    "1321100.batch|RUNNING|00:04:39|0:0",
+    "1321100.extern|RUNNING|00:04:39|0:0",
+    "1321145|PENDING|00:00:00|0:0"
   ],
   "next_update": {
     "scheduled": true,
@@ -279,6 +306,13 @@
       "start_cluster_time": "2026-10-13T15:00:22",
       "reason": "(BeginTime)"
     },
+    {
+      "id": "1321145",
+      "name": "simplefold-finalize",
+      "state": "PENDING",
+      "start_cluster_time": "N/A",
+      "reason": "(Dependency)"
+    },
     {
       "id": "1320625",
       "name": "simplefold-pdb",
@@ -287,39 +321,41 @@
       "reason": "w0001"
     },
     {
-      "id": "1320554",
-      "name": "simplefold-afesm",
+      "id": "1321100",
+      "name": "simplefold-afdb-bulk",
       "state": "RUNNING",
-      "start_cluster_time": "2026-10-13T14:08:50",
-      "reason": "w0004"
+      "start_cluster_time": "2026-10-13T14:39:44",
+      "reason": "w0002"
     }
   ],
   "queue_timezone": "America/New_York",
   "estimates": {
-    "afesm": {
-      "candidates_per_second": 2.5541216685616814,
-      "remaining_seconds": 331822.09384616587,
-      "planning_low_seconds": 248866.5703846244,
-      "planning_high_seconds": 497733.1407692488,
-      "finish_utc": "2026-10-17T14:35:09+00:00",
+    "afdb_bulk": {
+      "candidates_per_second": 0.39065419225799314,
+      "remaining_seconds": 2283.3493603235456,
+      "planning_low_seconds": 1712.5120202426592,
+      "planning_high_seconds": 3425.0240404853184,
+      "finish_utc": "2026-10-13T19:22:26+00:00",
       "basis": "change since previous snapshot",
+      "unit": "shards/s",
       "scope": "Completion of candidate attempts, not final eligible unique sequences"
     },
     "pdb": {
-      "candidates_per_second": 5.213349333987767,
-      "remaining_seconds": 30595.877962774222,
-      "planning_low_seconds": 22946.908472080668,
-      "planning_high_seconds": 45893.816944161335,
-      "finish_utc": "2026-10-14T02:54:42+00:00",
+      "candidates_per_second": 5.226490729071951,
+      "remaining_seconds": 29343.398457961506,
+      "planning_low_seconds": 22007.54884347113,
+      "planning_high_seconds": 44015.09768694226,
+      "finish_utc": "2026-10-14T02:53:26+00:00",
       "basis": "change since previous snapshot",
+      "unit": "entries/s",
       "scope": "Completion of candidate attempts, not final eligible unique sequences"
     }
   },
   "automation": [
     {
-      "stage": "AFESM and PDB collection",
-      "mode": "Automatic continuation",
-      "detail": "Collectors submit a successor at their 18-hour checkpoint until their configured candidate limits. Failures require attention."
+      "stage": "AFDB bulk and PDB collection",
+      "mode": "Running",
+      "detail": "Pinned AFDB-1.6M coordinate shards replace the API collector. Completed shard validation is checkpointed. PDB collection continues."
     },
     {
       "stage": "Progress updates",
@@ -328,8 +364,8 @@
     },
     {
       "stage": "Final deduplication and selection",
-      "mode": "Not queued",
-      "detail": "Requires completed source pool and a final selection job."
+      "mode": "Queued after collection",
+      "detail": "Job 1321145 waits for successful AFDB and PDB jobs. Prefer PDB for exact duplicate sequences; select up to one million."
     },
     {
       "stage": "ESM-C 6B production embeddings",
@@ -337,9 +373,9 @@
       "detail": "60-sequence pilot complete; full cache production has not been launched."
     },
     {
-      "stage": "Remaining uploads and final release",
-      "mode": "Not queued",
-      "detail": "SwissProt candidates are uploaded. AFESM/PDB shards and final release still need publishing jobs."
+      "stage": "Selected coordinates and final manifest upload",
+      "mode": "Included in finalizer",
+      "detail": "Automatically packs and publishes the selected AFDB/PDB coordinates after selection. SwissProt remains a separate preserved source."
     }
   ],
   "eta_note": "Throughput projections for candidate collection only. Planning ranges are 0.75\u20131.5 times the projection, not confidence intervals. Excludes future queue delays, outages, final curation, production embeddings and uploads. End-to-end completion is not yet estimated."

reports/progress.md

@@ -1,6 +1,6 @@
 # SimpleFoldData — collection and curation progress
 
-Updated **2026-10-13T18:24:47+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
+Updated **2026-10-13T18:44:23+00:00**. Target: **1,000,000 distinct sequences with validated structures**.
 
 Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 
@@ -10,9 +10,9 @@ Status: **BUILD IN PROGRESS — final million-chain release not ready**.
 | Author AFESM clusters indexed | 2,036,414 |
 | Author AFESM-E membership rows indexed | 8,616,595 |
 | Author SwissProt IDs indexed | 269,003 |
-| Coordinate-qualified candidates (before global deduplication) | 275,530 |
+| Coordinate-qualified candidates (before global deduplication) | 157,837 |
 | Final selected unique sequences | not yet measured |
-| Structure candidates uploaded | 263,278 |
+| Selected structures uploaded | 0 |
 | Sequences embedded | 60 |
 | Embedding bytes stored | 156,194,104 |
 
@@ -22,8 +22,9 @@ Source catalog counts are not counts of retrieved or training-ready structures.
 
 - **Author inventory:** author_inventory_complete; swissprot_author_rows=269,003, afesm_author_rows=2,036,414, targets=2,305,417, clusters=2,036,414, memberships=8,616,595, afesm_representatives_unmapped=0, members_with_multiple_clusters=0
 - **SwissProt:** complete; coordinate_qualified=263,278, confidence_rejected=5,698, absent_from_available_archive=27
-- **AFESM:** running; coordinate_qualified=2,262, source_unavailable=205, confidence_rejected=17, validation_rejected=2
-- **PDB:** running; entry_processed=3,710, coordinate_qualified=9,990, validation_rejected=2
+- **AFESM (superseded):** superseded; coordinate_qualified=4,477, source_unavailable=403, confidence_rejected=46, validation_rejected=2
+- **AFDB bulk:** running; coordinate_qualified=131,065, validation_rejected=50,375
+- **PDB:** running; entry_processed=9,854, coordinate_qualified=26,772, validation_rejected=2
 - **Final curation:** not started
 - **Upload:** swissprot_candidates_uploaded
 - **ESM-C 6B embeddings:** pilot_complete
@@ -55,12 +56,16 @@ JobID|State|Elapsed|ExitCode
 1320537|COMPLETED|00:02:11|0:0
 1320537.batch|COMPLETED|00:02:11|0:0
 1320537.extern|COMPLETED|00:02:11|0:0
-1320554|RUNNING|00:15:57|0:0
-1320554.batch|RUNNING|00:15:57|0:0
-1320554.extern|RUNNING|00:15:57|0:0
-1320625|RUNNING|00:11:30|0:0
-1320625.batch|RUNNING|00:11:30|0:0
-1320625.extern|RUNNING|00:11:30|0:0
+1320554|CANCELLED by 21014|00:31:03|0:0
+1320554.batch|CANCELLED|00:31:03|0:15
+1320554.extern|COMPLETED|00:31:03|0:0
+1320625|RUNNING|00:31:06|0:0
+1320625.batch|RUNNING|00:31:06|0:0
+1320625.extern|RUNNING|00:31:06|0:0
+1321100|RUNNING|00:04:39|0:0
+1321100.batch|RUNNING|00:04:39|0:0
+1321100.extern|RUNNING|00:04:39|0:0
+1321145|PENDING|00:00:00|0:0
 ```
 
 Next hourly update scheduled; remaining updates: 168.