diff --git a/extract/embeddings/go_mf/gvp/ids_test.txt b/extract/embeddings/go_mf/gvp/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85ab7b30fd8f1dbf720717964109e124fbea064e
--- /dev/null
+++ b/extract/embeddings/go_mf/gvp/ids_test.txt
@@ -0,0 +1,2904 @@
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diff --git a/extract/embeddings/go_mf/gvp/ids_train.txt b/extract/embeddings/go_mf/gvp/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e251777976c3965aca46a9f3e8aadc62cf6571d
--- /dev/null
+++ b/extract/embeddings/go_mf/gvp/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/go_mf/gvp/ids_valid.txt b/extract/embeddings/go_mf/gvp/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b22ca1f3cc60f2469d6cab66066a83153f68be30
--- /dev/null
+++ b/extract/embeddings/go_mf/gvp/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/go_mf/gvp/meta.json b/extract/embeddings/go_mf/gvp/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d18228b9b660d82dad5aea67bf274ddf1c972d9e
--- /dev/null
+++ b/extract/embeddings/go_mf/gvp/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "gvp",
+ "family": "patched",
+ "target": "gvp_inproc",
+ "weights": "random",
+ "rule": "scalar channels + vector norms (invariant), masked mean",
+ "env": "base",
+ "weights_sha256": "4199962f00f771e2",
+ "seed": 20260919,
+ "n_parameters": 476935,
+ "inputs_passed": "backbone coordinates and residue identity",
+ "patch": "patched/gvp_inproc.py",
+ "task": "go_mf",
+ "date": "2026-09-20 12:49",
+ "seconds": 33.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2904,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10404,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10404,
+  "numerical_rank": 115,
+  "max_abs": 2.875061511993408
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.031185459542244547,
+  "rel_change_coord_swap": 0.0063201345160243646,
+  "rel_change_seq_shuffle": 0.0027774681296060446,
+  "rel_change_rigid_motion": 8.399049766645085e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/go_mf/mace/ids_test.txt b/extract/embeddings/go_mf/mace/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85ab7b30fd8f1dbf720717964109e124fbea064e
--- /dev/null
+++ b/extract/embeddings/go_mf/mace/ids_test.txt
@@ -0,0 +1,2904 @@
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diff --git a/extract/embeddings/go_mf/mace/ids_valid.txt b/extract/embeddings/go_mf/mace/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b22ca1f3cc60f2469d6cab66066a83153f68be30
--- /dev/null
+++ b/extract/embeddings/go_mf/mace/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/go_mf/mace/meta.json b/extract/embeddings/go_mf/mace/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7b796224f51e322cf4876a85a53704333f0d7faa
--- /dev/null
+++ b/extract/embeddings/go_mf/mace/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "mace",
+ "family": "registry",
+ "target": "mace",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "e8e9d6fd9722cc4e",
+ "n_parameters": 584064,
+ "task": "go_mf",
+ "date": "2026-09-20 12:48",
+ "seconds": 21.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2904,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10404,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10404,
+  "numerical_rank": 127,
+  "max_abs": 1.0530033111572266
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.014915865242322838,
+  "rel_change_coord_swap": 0.05683945173750876,
+  "rel_change_seq_shuffle": 0.0523291422188011,
+  "rel_change_rigid_motion": 1.3602486243731065e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_test.txt b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85ab7b30fd8f1dbf720717964109e124fbea064e
--- /dev/null
+++ b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_test.txt
@@ -0,0 +1,2904 @@
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diff --git a/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_train.txt b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e251777976c3965aca46a9f3e8aadc62cf6571d
--- /dev/null
+++ b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_train.txt
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diff --git a/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b22ca1f3cc60f2469d6cab66066a83153f68be30
--- /dev/null
+++ b/extract/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/go_mf/prottrans_t5_xl_u50/meta.json b/extract/embeddings/go_mf/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a6a09eb58fee6ed15375d63b4e7fff6fa65b118a
--- /dev/null
+++ b/extract/embeddings/go_mf/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "prottrans_t5_xl_u50",
+ "family": "hf_plm",
+ "target": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "checkpoint_revision": "94a6abc029ae13029317b140b7424e012bf8dfbf",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208141824,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "go_mf",
+ "date": "2026-09-20 12:34",
+ "seconds": 125.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2904,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10404,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10389,
+  "numerical_rank": 1024,
+  "max_abs": 0.574646532535553
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.7503630666663541,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/ankh_base/ids_test.txt b/extract/embeddings/membrane_soluble/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ankh_base/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/ankh_base/ids_train.txt b/extract/embeddings/membrane_soluble/ankh_base/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ankh_base/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/ankh_base/ids_valid.txt b/extract/embeddings/membrane_soluble/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ankh_base/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/ankh_base/meta.json b/extract/embeddings/membrane_soluble/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..fcaa1f7d7633e8c50ab90c1a2254f2dc9517c637
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ankh_base/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "ankh_base",
+ "family": "hf_plm",
+ "target": "ElnaggarLab/ankh-base",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "ElnaggarLab/ankh-base",
+ "checkpoint_revision": "d99cb6b966530dfc2ae96bc69d9255c2a07308b0",
+ "dtype": "float32",
+ "hidden_size": 768,
+ "n_layers": 48,
+ "n_parameters": 453170688,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "membrane_soluble",
+ "date": "2026-09-20 16:15",
+ "seconds": 330.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 768,
+  "max_abs": 0.6288496851921082
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.5002829140921271,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/ankh_base/ids_test.txt b/extract/embeddings/stability/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/ankh_base/ids_test.txt
@@ -0,0 +1,3000 @@
+EEHEE_rd3_0037.pdb_A19G__test_000004
+EEHEE_rd3_0037.pdb_A19H__test_000005
+EEHEE_rd3_0037.pdb_A19I__test_000006
+EEHEE_rd3_0037.pdb_A19S__test_000014
+EEHEE_rd3_0037.pdb_A19T__test_000015
+EEHEE_rd3_0037.pdb_A19Y__test_000018
+EEHEE_rd3_0037.pdb_A20D__test_000019
+EEHEE_rd3_0037.pdb_A20G__test_000022
+EEHEE_rd3_0037.pdb_A20H__test_000023
+EEHEE_rd3_0037.pdb_A20M__test_000027
+EEHEE_rd3_0037.pdb_A20V__test_000034
+EEHEE_rd3_0037.pdb_A22G__test_000040
+EEHEE_rd3_0037.pdb_A22I__test_000042
+EEHEE_rd3_0037.pdb_A22L__test_000044
+EEHEE_rd3_0037.pdb_A23H__test_000059
+EEHEE_rd3_0037.pdb_A23K__test_000061
+EEHEE_rd3_0037.pdb_A23N__test_000064
+EEHEE_rd3_0037.pdb_A23P__test_000065
+EEHEE_rd3_0037.pdb_A23Y__test_000072
+EEHEE_rd3_0037.pdb_D29E__test_000074
+EEHEE_rd3_0037.pdb_D29Y__test_000090
+EEHEE_rd3_0037.pdb_E17W__test_000107
+EEHEE_rd3_0037.pdb_E17Y__test_000108
+EEHEE_rd3_0037.pdb_E31G__test_000112
+EEHEE_rd3_0037.pdb_E31I__test_000114
+EEHEE_rd3_0037.pdb_E31L__test_000116
+EEHEE_rd3_0037.pdb_E31N__test_000118
+EEHEE_rd3_0037.pdb_E31Q__test_000120
+EEHEE_rd3_0037.pdb_E31T__test_000123
+EEHEE_rd3_0037.pdb_E31V__test_000124
+EEHEE_rd3_0037.pdb_E31W__test_000125
+EEHEE_rd3_0037.pdb_E9I__test_000132
+EEHEE_rd3_0037.pdb_E9K__test_000133
+EEHEE_rd3_0037.pdb_E9W__test_000143
+EEHEE_rd3_0037.pdb_G36A__test_000145
+EEHEE_rd3_0037.pdb_G36I__test_000150
+EEHEE_rd3_0037.pdb_G36M__test_000153
+EEHEE_rd3_0037.pdb_G36R__test_000157
+EEHEE_rd3_0037.pdb_G7A__test_000163
+EEHEE_rd3_0037.pdb_G7E__test_000165
+EEHEE_rd3_0037.pdb_G7M__test_000171
+EEHEE_rd3_0037.pdb_G7P__test_000173
+EEHEE_rd3_0037.pdb_G7W__test_000179
+EEHEE_rd3_0037.pdb_H35I__test_000186
+EEHEE_rd3_0037.pdb_H35K__test_000187
+EEHEE_rd3_0037.pdb_H35P__test_000191
+EEHEE_rd3_0037.pdb_H35R__test_000193
+EEHEE_rd3_0037.pdb_H35S__test_000194
+EEHEE_rd3_0037.pdb_I34Y__test_000216
+EEHEE_rd3_0037.pdb_I3D__test_000218
+EEHEE_rd3_0037.pdb_I3E__test_000219
+EEHEE_rd3_0037.pdb_I3K__test_000223
+EEHEE_rd3_0037.pdb_I3M__test_000225
+EEHEE_rd3_0037.pdb_I3T__test_000231
+EEHEE_rd3_0037.pdb_K21F__test_000238
+EEHEE_rd3_0037.pdb_K21H__test_000240
+EEHEE_rd3_0037.pdb_K21Q__test_000246
+EEHEE_rd3_0037.pdb_K24A__test_000253
+EEHEE_rd3_0037.pdb_K24D__test_000254
+EEHEE_rd3_0037.pdb_K24G__test_000257
+EEHEE_rd3_0037.pdb_K24H__test_000258
+EEHEE_rd3_0037.pdb_K24W__test_000269
+EEHEE_rd3_0037.pdb_K25G__test_000275
+EEHEE_rd3_0037.pdb_K25V__test_000286
+EEHEE_rd3_0037.pdb_K40A__test_000289
+EEHEE_rd3_0037.pdb_K40D__test_000290
+EEHEE_rd3_0037.pdb_K40E__test_000291
+EEHEE_rd3_0037.pdb_K40I__test_000295
+EEHEE_rd3_0037.pdb_K40L__test_000296
+EEHEE_rd3_0037.pdb_K4E__test_000309
+EEHEE_rd3_0037.pdb_K4M__test_000315
+EEHEE_rd3_0037.pdb_K4P__test_000317
+EEHEE_rd3_0037.pdb_K4W__test_000323
+EEHEE_rd3_0037.pdb_L14H__test_000330
+EEHEE_rd3_0037.pdb_L14R__test_000337
+EEHEE_rd3_0037.pdb_L14V__test_000340
+EEHEE_rd3_0037.pdb_N37D__test_000344
+EEHEE_rd3_0037.pdb_N6A__test_000361
+EEHEE_rd3_0037.pdb_N6F__test_000364
+EEHEE_rd3_0037.pdb_N6G__test_000365
+EEHEE_rd3_0037.pdb_N6R__test_000373
+EEHEE_rd3_0037.pdb_N6Y__test_000378
+EEHEE_rd3_0037.pdb_P13D__test_000380
+EEHEE_rd3_0037.pdb_P13H__test_000384
+EEHEE_rd3_0037.pdb_P13M__test_000388
+EEHEE_rd3_0037.pdb_P13V__test_000394
+EEHEE_rd3_0037.pdb_P16L__test_000405
+EEHEE_rd3_0037.pdb_P16Q__test_000408
+EEHEE_rd3_0037.pdb_P16Y__test_000414
+EEHEE_rd3_0037.pdb_P28F__test_000418
+EEHEE_rd3_0037.pdb_P28I__test_000421
+EEHEE_rd3_0037.pdb_P28M__test_000424
+EEHEE_rd3_0037.pdb_P28Q__test_000426
+EEHEE_rd3_0037.pdb_P28S__test_000428
+EEHEE_rd3_0037.pdb_Q18P__test_000444
+EEHEE_rd3_0037.pdb_Q18T__test_000447
+EEHEE_rd3_0037.pdb_Q33A__test_000451
+EEHEE_rd3_0037.pdb_Q33E__test_000453
+EEHEE_rd3_0037.pdb_Q33H__test_000456
+EEHEE_rd3_0037.pdb_Q33L__test_000459
+EEHEE_rd3_0037.pdb_Q33S__test_000464
+EEHEE_rd3_0037.pdb_Q33W__test_000467
+EEHEE_rd3_0037.pdb_Q8A__test_000469
+EEHEE_rd3_0037.pdb_Q8D__test_000470
+EEHEE_rd3_0037.pdb_Q8F__test_000472
+EEHEE_rd3_0037.pdb_Q8M__test_000478
+EEHEE_rd3_0037.pdb_Q8R__test_000481
+EEHEE_rd3_0037.pdb_R26E__test_000489
+EEHEE_rd3_0037.pdb_R26G__test_000491
+EEHEE_rd3_0037.pdb_R43F__test_000508
+EEHEE_rd3_0037.pdb_R43P__test_000516
+EEHEE_rd3_0037.pdb_R43S__test_000518
+EEHEE_rd3_0037.pdb_S15D__test_000524
+EEHEE_rd3_0037.pdb_S15H__test_000528
+EEHEE_rd3_0037.pdb_S15N__test_000533
+EEHEE_rd3_0037.pdb_S15T__test_000537
+EEHEE_rd3_0037.pdb_T11G__test_000545
+EEHEE_rd3_0037.pdb_T11K__test_000548
+EEHEE_rd3_0037.pdb_T11M__test_000550
+EEHEE_rd3_0037.pdb_T11N__test_000551
+EEHEE_rd3_0037.pdb_T1A__test_000559
+EEHEE_rd3_0037.pdb_T1H__test_000564
+EEHEE_rd3_0037.pdb_T1P__test_000570
+EEHEE_rd3_0037.pdb_T2A__test_000577
+EEHEE_rd3_0037.pdb_T2F__test_000580
+EEHEE_rd3_0037.pdb_T2H__test_000582
+EEHEE_rd3_0037.pdb_T2K__test_000584
+EEHEE_rd3_0037.pdb_T2M__test_000586
+EEHEE_rd3_0037.pdb_T2N__test_000587
+EEHEE_rd3_0037.pdb_T2S__test_000591
+EEHEE_rd3_0037.pdb_T2V__test_000592
+EEHEE_rd3_0037.pdb_T38D__test_000596
+EEHEE_rd3_0037.pdb_T38G__test_000599
+EEHEE_rd3_0037.pdb_T38H__test_000600
+EEHEE_rd3_0037.pdb_T38R__test_000608
+EEHEE_rd3_0037.pdb_T38Y__test_000612
+EEHEE_rd3_0037.pdb_T42F__test_000616
+EEHEE_rd3_0037.pdb_T42K__test_000620
+EEHEE_rd3_0037.pdb_T42Q__test_000625
+EEHEE_rd3_0037.pdb_T42R__test_000626
+EEHEE_rd3_0037.pdb_T42S__test_000627
+EEHEE_rd3_0037.pdb_V12A__test_000631
+EEHEE_rd3_0037.pdb_V12E__test_000633
+EEHEE_rd3_0037.pdb_V12G__test_000635
+EEHEE_rd3_0037.pdb_V12H__test_000636
+EEHEE_rd3_0037.pdb_V12Y__test_000648
+EEHEE_rd3_0037.pdb_V32A__test_000649
+EEHEE_rd3_0037.pdb_V32E__test_000651
+EEHEE_rd3_0037.pdb_V32G__test_000653
+EEHEE_rd3_0037.pdb_V32H__test_000654
+EEHEE_rd3_0037.pdb_V32R__test_000662
+EEHEE_rd3_0037.pdb_V32T__test_000664
+EEHEE_rd3_0037.pdb_V39D__test_000668
+EEHEE_rd3_0037.pdb_V39Q__test_000679
+EEHEE_rd3_0037.pdb_V39T__test_000682
+EEHEE_rd3_0037.pdb_V39Y__test_000684
+EEHEE_rd3_0037.pdb_V41P__test_000696
+EEHEE_rd3_0037.pdb_V41Q__test_000697
+EEHEE_rd3_0037.pdb_V41S__test_000699
+EEHEE_rd3_0037.pdb_V41W__test_000701
+EEHEE_rd3_0037.pdb_V41Y__test_000702
+EEHEE_rd3_0037.pdb_V5D__test_000704
+EEHEE_rd3_0037.pdb_W27D__test_000722
+EEHEE_rd3_0037.pdb_W27K__test_000728
+EEHEE_rd3_0037.pdb_W27R__test_000734
+EEHEE_rd3_0037.pdb_W27Y__test_000738
+EEHEE_rd3_0037.pdb_Y10D__test_000740
+EEHEE_rd3_0037.pdb_Y10H__test_000744
+EEHEE_rd3_0037.pdb_Y10I__test_000745
+EEHEE_rd3_0037.pdb_Y10K__test_000746
+EEHEE_rd3_0037.pdb_Y10L__test_000747
+EEHEE_rd3_0037.pdb_Y30F__test_000760
+EEHEE_rd3_0037.pdb_Y30I__test_000763
+EEHEE_rd3_0037.pdb_Y30M__test_000766
+EEHEE_rd3_0037.pdb_Y30Q__test_000769
+EEHEE_rd3_0037.pdb_Y30S__test_000771
+EEHEE_rd3_0037.pdb_Y30W__test_000774
+EEHEE_rd3_1498.pdb_A18E__test_000777
+EEHEE_rd3_1498.pdb_A18L__test_000783
+EEHEE_rd3_1498.pdb_A18M__test_000784
+EEHEE_rd3_1498.pdb_A18V__test_000791
+EEHEE_rd3_1498.pdb_A21F__test_000796
+EEHEE_rd3_1498.pdb_A21G__test_000797
+EEHEE_rd3_1498.pdb_A21K__test_000800
+EEHEE_rd3_1498.pdb_A21Q__test_000805
+EEHEE_rd3_1498.pdb_A22D__test_000812
+EEHEE_rd3_1498.pdb_A22H__test_000816
+EEHEE_rd3_1498.pdb_A22L__test_000819
+EEHEE_rd3_1498.pdb_A22T__test_000826
+EEHEE_rd3_1498.pdb_A26F__test_000832
+EEHEE_rd3_1498.pdb_A26K__test_000836
+EEHEE_rd3_1498.pdb_A26P__test_000840
+EEHEE_rd3_1498.pdb_A26Q__test_000841
+EEHEE_rd3_1498.pdb_A26R__test_000842
+EEHEE_rd3_1498.pdb_A26S__test_000843
+EEHEE_rd3_1498.pdb_E16L__test_000855
+EEHEE_rd3_1498.pdb_E16W__test_000864
+EEHEE_rd3_1498.pdb_E32M__test_000874
+EEHEE_rd3_1498.pdb_F25K__test_000890
+EEHEE_rd3_1498.pdb_F25T__test_000898
+EEHEE_rd3_1498.pdb_F25W__test_000900
+EEHEE_rd3_1498.pdb_F25Y__test_000901
+EEHEE_rd3_1498.pdb_G1A__test_000902
+EEHEE_rd3_1498.pdb_G1E__test_000904
+EEHEE_rd3_1498.pdb_G1R__test_000914
+EEHEE_rd3_1498.pdb_G1V__test_000917
+EEHEE_rd3_1498.pdb_G1Y__test_000919
+EEHEE_rd3_1498.pdb_G37E__test_000922
+EEHEE_rd3_1498.pdb_G37Y__test_000937
+EEHEE_rd3_1498.pdb_G7A__test_000938
+EEHEE_rd3_1498.pdb_G7H__test_000942
+EEHEE_rd3_1498.pdb_G7N__test_000947
+EEHEE_rd3_1498.pdb_G7W__test_000954
+EEHEE_rd3_1498.pdb_H36A__test_000956
+EEHEE_rd3_1498.pdb_H36P__test_000966
+EEHEE_rd3_1498.pdb_H36T__test_000970
+EEHEE_rd3_1498.pdb_H36W__test_000972
+EEHEE_rd3_1498.pdb_H41Y__test_000991
+EEHEE_rd3_1498.pdb_H43A__test_000992
+EEHEE_rd3_1498.pdb_H43I__test_000997
+EEHEE_rd3_1498.pdb_H43L__test_000999
+EEHEE_rd3_1498.pdb_H43S__test_001005
+EEHEE_rd3_1498.pdb_H4G__test_001014
+EEHEE_rd3_1498.pdb_H4I__test_001015
+EEHEE_rd3_1498.pdb_H4K__test_001016
+EEHEE_rd3_1498.pdb_H4L__test_001017
+EEHEE_rd3_1498.pdb_H4M__test_001018
+EEHEE_rd3_1498.pdb_H4P__test_001020
+EEHEE_rd3_1498.pdb_H4Q__test_001021
+EEHEE_rd3_1498.pdb_H4V__test_001025
+EEHEE_rd3_1498.pdb_I19A__test_001028
+EEHEE_rd3_1498.pdb_I19E__test_001030
+EEHEE_rd3_1498.pdb_I19F__test_001031
+EEHEE_rd3_1498.pdb_I19R__test_001040
+EEHEE_rd3_1498.pdb_K11D__test_001047
+EEHEE_rd3_1498.pdb_K11G__test_001050
+EEHEE_rd3_1498.pdb_K11P__test_001056
+EEHEE_rd3_1498.pdb_K11R__test_001058
+EEHEE_rd3_1498.pdb_K11T__test_001060
+EEHEE_rd3_1498.pdb_K17D__test_001065
+EEHEE_rd3_1498.pdb_K17V__test_001079
+EEHEE_rd3_1498.pdb_K20A__test_001082
+EEHEE_rd3_1498.pdb_K20G__test_001086
+EEHEE_rd3_1498.pdb_K20M__test_001090
+EEHEE_rd3_1498.pdb_K20P__test_001092
+EEHEE_rd3_1498.pdb_K20T__test_001096
+EEHEE_rd3_1498.pdb_K20Y__test_001099
+EEHEE_rd3_1498.pdb_K23E__test_001102
+EEHEE_rd3_1498.pdb_K23F__test_001103
+EEHEE_rd3_1498.pdb_K23L__test_001107
+EEHEE_rd3_1498.pdb_K23M__test_001108
+EEHEE_rd3_1498.pdb_K23R__test_001112
+EEHEE_rd3_1498.pdb_K23T__test_001114
+EEHEE_rd3_1498.pdb_K23Y__test_001117
+EEHEE_rd3_1498.pdb_K24E__test_001120
+EEHEE_rd3_1498.pdb_K24I__test_001124
+EEHEE_rd3_1498.pdb_K24W__test_001134
+EEHEE_rd3_1498.pdb_K24Y__test_001135
+EEHEE_rd3_1498.pdb_K27M__test_001144
+EEHEE_rd3_1498.pdb_K27Q__test_001147
+EEHEE_rd3_1498.pdb_K28D__test_001155
+EEHEE_rd3_1498.pdb_K28E__test_001156
+EEHEE_rd3_1498.pdb_K28I__test_001160
+EEHEE_rd3_1498.pdb_K28Q__test_001165
+EEHEE_rd3_1498.pdb_K28R__test_001166
+EEHEE_rd3_1498.pdb_L15E__test_001174
+EEHEE_rd3_1498.pdb_L15N__test_001181
+EEHEE_rd3_1498.pdb_L15R__test_001184
+EEHEE_rd3_1498.pdb_L15T__test_001186
+EEHEE_rd3_1498.pdb_L15W__test_001188
+EEHEE_rd3_1498.pdb_L31D__test_001191
+EEHEE_rd3_1498.pdb_L31P__test_001200
+EEHEE_rd3_1498.pdb_L31V__test_001205
+EEHEE_rd3_1498.pdb_L5F__test_001229
+EEHEE_rd3_1498.pdb_L5H__test_001231
+EEHEE_rd3_1498.pdb_L5I__test_001232
+EEHEE_rd3_1498.pdb_L5K__test_001233
+EEHEE_rd3_1498.pdb_L5M__test_001234
+EEHEE_rd3_1498.pdb_L5S__test_001239
+EEHEE_rd3_1498.pdb_L5V__test_001241
+EEHEE_rd3_1498.pdb_L5W__test_001242
+EEHEE_rd3_1498.pdb_N30I__test_001250
+EEHEE_rd3_1498.pdb_N30S__test_001257
+EEHEE_rd3_1498.pdb_N30T__test_001258
+EEHEE_rd3_1498.pdb_N30W__test_001260
+EEHEE_rd3_1498.pdb_N30Y__test_001261
+EEHEE_rd3_1498.pdb_N38A__test_001262
+EEHEE_rd3_1498.pdb_N38P__test_001272
+EEHEE_rd3_1498.pdb_N38Q__test_001273
+EEHEE_rd3_1498.pdb_N6I__test_001286
+EEHEE_rd3_1498.pdb_N6M__test_001289
+EEHEE_rd3_1498.pdb_N6P__test_001290
+EEHEE_rd3_1498.pdb_N6R__test_001292
+EEHEE_rd3_1498.pdb_N6V__test_001295
+EEHEE_rd3_1498.pdb_N6W__test_001296
+EEHEE_rd3_1498.pdb_P13H__test_001303
+EEHEE_rd3_1498.pdb_P13K__test_001305
+EEHEE_rd3_1498.pdb_P13Q__test_001309
+EEHEE_rd3_1498.pdb_P13R__test_001310
+EEHEE_rd3_1498.pdb_P13T__test_001312
+EEHEE_rd3_1498.pdb_P13V__test_001313
+EEHEE_rd3_1498.pdb_P13W__test_001314
+EEHEE_rd3_1498.pdb_P13Y__test_001315
+EEHEE_rd3_1498.pdb_Q34F__test_001319
+EEHEE_rd3_1498.pdb_Q34H__test_001321
+EEHEE_rd3_1498.pdb_Q34I__test_001322
+EEHEE_rd3_1498.pdb_Q34Y__test_001333
+EEHEE_rd3_1498.pdb_S14D__test_001335
+EEHEE_rd3_1498.pdb_S14E__test_001336
+EEHEE_rd3_1498.pdb_S14H__test_001339
+EEHEE_rd3_1498.pdb_S14I__test_001340
+EEHEE_rd3_1498.pdb_S14P__test_001345
+EEHEE_rd3_1498.pdb_T2F__test_001355
+EEHEE_rd3_1498.pdb_T2G__test_001356
+EEHEE_rd3_1498.pdb_T2I__test_001358
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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diff --git a/extract/embeddings/stability/ankh_base/ids_valid.txt b/extract/embeddings/stability/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
--- /dev/null
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diff --git a/extract/embeddings/stability/ankh_base/meta.json b/extract/embeddings/stability/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..74da7ca6ede2d0bfe0296c54c481ac18886ba1b4
--- /dev/null
+++ b/extract/embeddings/stability/ankh_base/meta.json
@@ -0,0 +1,43 @@
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+ "checkpoint_revision": "d99cb6b966530dfc2ae96bc69d9255c2a07308b0",
+ "dtype": "float32",
+ "hidden_size": 768,
+ "n_layers": 48,
+ "n_parameters": 453170688,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:54",
+ "seconds": 31.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 768,
+  "max_abs": 0.8662146925926208
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.5002829140921271,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/cdconv/ids_test.txt b/extract/embeddings/stability/cdconv/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/cdconv/ids_test.txt
@@ -0,0 +1,3000 @@
+EEHEE_rd3_0037.pdb_A19G__test_000004
+EEHEE_rd3_0037.pdb_A19H__test_000005
+EEHEE_rd3_0037.pdb_A19I__test_000006
+EEHEE_rd3_0037.pdb_A19S__test_000014
+EEHEE_rd3_0037.pdb_A19T__test_000015
+EEHEE_rd3_0037.pdb_A19Y__test_000018
+EEHEE_rd3_0037.pdb_A20D__test_000019
+EEHEE_rd3_0037.pdb_A20G__test_000022
+EEHEE_rd3_0037.pdb_A20H__test_000023
+EEHEE_rd3_0037.pdb_A20M__test_000027
+EEHEE_rd3_0037.pdb_A20V__test_000034
+EEHEE_rd3_0037.pdb_A22G__test_000040
+EEHEE_rd3_0037.pdb_A22I__test_000042
+EEHEE_rd3_0037.pdb_A22L__test_000044
+EEHEE_rd3_0037.pdb_A23H__test_000059
+EEHEE_rd3_0037.pdb_A23K__test_000061
+EEHEE_rd3_0037.pdb_A23N__test_000064
+EEHEE_rd3_0037.pdb_A23P__test_000065
+EEHEE_rd3_0037.pdb_A23Y__test_000072
+EEHEE_rd3_0037.pdb_D29E__test_000074
+EEHEE_rd3_0037.pdb_D29Y__test_000090
+EEHEE_rd3_0037.pdb_E17W__test_000107
+EEHEE_rd3_0037.pdb_E17Y__test_000108
+EEHEE_rd3_0037.pdb_E31G__test_000112
+EEHEE_rd3_0037.pdb_E31I__test_000114
+EEHEE_rd3_0037.pdb_E31L__test_000116
+EEHEE_rd3_0037.pdb_E31N__test_000118
+EEHEE_rd3_0037.pdb_E31Q__test_000120
+EEHEE_rd3_0037.pdb_E31T__test_000123
+EEHEE_rd3_0037.pdb_E31V__test_000124
+EEHEE_rd3_0037.pdb_E31W__test_000125
+EEHEE_rd3_0037.pdb_E9I__test_000132
+EEHEE_rd3_0037.pdb_E9K__test_000133
+EEHEE_rd3_0037.pdb_E9W__test_000143
+EEHEE_rd3_0037.pdb_G36A__test_000145
+EEHEE_rd3_0037.pdb_G36I__test_000150
+EEHEE_rd3_0037.pdb_G36M__test_000153
+EEHEE_rd3_0037.pdb_G36R__test_000157
+EEHEE_rd3_0037.pdb_G7A__test_000163
+EEHEE_rd3_0037.pdb_G7E__test_000165
+EEHEE_rd3_0037.pdb_G7M__test_000171
+EEHEE_rd3_0037.pdb_G7P__test_000173
+EEHEE_rd3_0037.pdb_G7W__test_000179
+EEHEE_rd3_0037.pdb_H35I__test_000186
+EEHEE_rd3_0037.pdb_H35K__test_000187
+EEHEE_rd3_0037.pdb_H35P__test_000191
+EEHEE_rd3_0037.pdb_H35R__test_000193
+EEHEE_rd3_0037.pdb_H35S__test_000194
+EEHEE_rd3_0037.pdb_I34Y__test_000216
+EEHEE_rd3_0037.pdb_I3D__test_000218
+EEHEE_rd3_0037.pdb_I3E__test_000219
+EEHEE_rd3_0037.pdb_I3K__test_000223
+EEHEE_rd3_0037.pdb_I3M__test_000225
+EEHEE_rd3_0037.pdb_I3T__test_000231
+EEHEE_rd3_0037.pdb_K21F__test_000238
+EEHEE_rd3_0037.pdb_K21H__test_000240
+EEHEE_rd3_0037.pdb_K21Q__test_000246
+EEHEE_rd3_0037.pdb_K24A__test_000253
+EEHEE_rd3_0037.pdb_K24D__test_000254
+EEHEE_rd3_0037.pdb_K24G__test_000257
+EEHEE_rd3_0037.pdb_K24H__test_000258
+EEHEE_rd3_0037.pdb_K24W__test_000269
+EEHEE_rd3_0037.pdb_K25G__test_000275
+EEHEE_rd3_0037.pdb_K25V__test_000286
+EEHEE_rd3_0037.pdb_K40A__test_000289
+EEHEE_rd3_0037.pdb_K40D__test_000290
+EEHEE_rd3_0037.pdb_K40E__test_000291
+EEHEE_rd3_0037.pdb_K40I__test_000295
+EEHEE_rd3_0037.pdb_K40L__test_000296
+EEHEE_rd3_0037.pdb_K4E__test_000309
+EEHEE_rd3_0037.pdb_K4M__test_000315
+EEHEE_rd3_0037.pdb_K4P__test_000317
+EEHEE_rd3_0037.pdb_K4W__test_000323
+EEHEE_rd3_0037.pdb_L14H__test_000330
+EEHEE_rd3_0037.pdb_L14R__test_000337
+EEHEE_rd3_0037.pdb_L14V__test_000340
+EEHEE_rd3_0037.pdb_N37D__test_000344
+EEHEE_rd3_0037.pdb_N6A__test_000361
+EEHEE_rd3_0037.pdb_N6F__test_000364
+EEHEE_rd3_0037.pdb_N6G__test_000365
+EEHEE_rd3_0037.pdb_N6R__test_000373
+EEHEE_rd3_0037.pdb_N6Y__test_000378
+EEHEE_rd3_0037.pdb_P13D__test_000380
+EEHEE_rd3_0037.pdb_P13H__test_000384
+EEHEE_rd3_0037.pdb_P13M__test_000388
+EEHEE_rd3_0037.pdb_P13V__test_000394
+EEHEE_rd3_0037.pdb_P16L__test_000405
+EEHEE_rd3_0037.pdb_P16Q__test_000408
+EEHEE_rd3_0037.pdb_P16Y__test_000414
+EEHEE_rd3_0037.pdb_P28F__test_000418
+EEHEE_rd3_0037.pdb_P28I__test_000421
+EEHEE_rd3_0037.pdb_P28M__test_000424
+EEHEE_rd3_0037.pdb_P28Q__test_000426
+EEHEE_rd3_0037.pdb_P28S__test_000428
+EEHEE_rd3_0037.pdb_Q18P__test_000444
+EEHEE_rd3_0037.pdb_Q18T__test_000447
+EEHEE_rd3_0037.pdb_Q33A__test_000451
+EEHEE_rd3_0037.pdb_Q33E__test_000453
+EEHEE_rd3_0037.pdb_Q33H__test_000456
+EEHEE_rd3_0037.pdb_Q33L__test_000459
+EEHEE_rd3_0037.pdb_Q33S__test_000464
+EEHEE_rd3_0037.pdb_Q33W__test_000467
+EEHEE_rd3_0037.pdb_Q8A__test_000469
+EEHEE_rd3_0037.pdb_Q8D__test_000470
+EEHEE_rd3_0037.pdb_Q8F__test_000472
+EEHEE_rd3_0037.pdb_Q8M__test_000478
+EEHEE_rd3_0037.pdb_Q8R__test_000481
+EEHEE_rd3_0037.pdb_R26E__test_000489
+EEHEE_rd3_0037.pdb_R26G__test_000491
+EEHEE_rd3_0037.pdb_R43F__test_000508
+EEHEE_rd3_0037.pdb_R43P__test_000516
+EEHEE_rd3_0037.pdb_R43S__test_000518
+EEHEE_rd3_0037.pdb_S15D__test_000524
+EEHEE_rd3_0037.pdb_S15H__test_000528
+EEHEE_rd3_0037.pdb_S15N__test_000533
+EEHEE_rd3_0037.pdb_S15T__test_000537
+EEHEE_rd3_0037.pdb_T11G__test_000545
+EEHEE_rd3_0037.pdb_T11K__test_000548
+EEHEE_rd3_0037.pdb_T11M__test_000550
+EEHEE_rd3_0037.pdb_T11N__test_000551
+EEHEE_rd3_0037.pdb_T1A__test_000559
+EEHEE_rd3_0037.pdb_T1H__test_000564
+EEHEE_rd3_0037.pdb_T1P__test_000570
+EEHEE_rd3_0037.pdb_T2A__test_000577
+EEHEE_rd3_0037.pdb_T2F__test_000580
+EEHEE_rd3_0037.pdb_T2H__test_000582
+EEHEE_rd3_0037.pdb_T2K__test_000584
+EEHEE_rd3_0037.pdb_T2M__test_000586
+EEHEE_rd3_0037.pdb_T2N__test_000587
+EEHEE_rd3_0037.pdb_T2S__test_000591
+EEHEE_rd3_0037.pdb_T2V__test_000592
+EEHEE_rd3_0037.pdb_T38D__test_000596
+EEHEE_rd3_0037.pdb_T38G__test_000599
+EEHEE_rd3_0037.pdb_T38H__test_000600
+EEHEE_rd3_0037.pdb_T38R__test_000608
+EEHEE_rd3_0037.pdb_T38Y__test_000612
+EEHEE_rd3_0037.pdb_T42F__test_000616
+EEHEE_rd3_0037.pdb_T42K__test_000620
+EEHEE_rd3_0037.pdb_T42Q__test_000625
+EEHEE_rd3_0037.pdb_T42R__test_000626
+EEHEE_rd3_0037.pdb_T42S__test_000627
+EEHEE_rd3_0037.pdb_V12A__test_000631
+EEHEE_rd3_0037.pdb_V12E__test_000633
+EEHEE_rd3_0037.pdb_V12G__test_000635
+EEHEE_rd3_0037.pdb_V12H__test_000636
+EEHEE_rd3_0037.pdb_V12Y__test_000648
+EEHEE_rd3_0037.pdb_V32A__test_000649
+EEHEE_rd3_0037.pdb_V32E__test_000651
+EEHEE_rd3_0037.pdb_V32G__test_000653
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+EEHEE_rd3_0037.pdb_V32R__test_000662
+EEHEE_rd3_0037.pdb_V32T__test_000664
+EEHEE_rd3_0037.pdb_V39D__test_000668
+EEHEE_rd3_0037.pdb_V39Q__test_000679
+EEHEE_rd3_0037.pdb_V39T__test_000682
+EEHEE_rd3_0037.pdb_V39Y__test_000684
+EEHEE_rd3_0037.pdb_V41P__test_000696
+EEHEE_rd3_0037.pdb_V41Q__test_000697
+EEHEE_rd3_0037.pdb_V41S__test_000699
+EEHEE_rd3_0037.pdb_V41W__test_000701
+EEHEE_rd3_0037.pdb_V41Y__test_000702
+EEHEE_rd3_0037.pdb_V5D__test_000704
+EEHEE_rd3_0037.pdb_W27D__test_000722
+EEHEE_rd3_0037.pdb_W27K__test_000728
+EEHEE_rd3_0037.pdb_W27R__test_000734
+EEHEE_rd3_0037.pdb_W27Y__test_000738
+EEHEE_rd3_0037.pdb_Y10D__test_000740
+EEHEE_rd3_0037.pdb_Y10H__test_000744
+EEHEE_rd3_0037.pdb_Y10I__test_000745
+EEHEE_rd3_0037.pdb_Y10K__test_000746
+EEHEE_rd3_0037.pdb_Y10L__test_000747
+EEHEE_rd3_0037.pdb_Y30F__test_000760
+EEHEE_rd3_0037.pdb_Y30I__test_000763
+EEHEE_rd3_0037.pdb_Y30M__test_000766
+EEHEE_rd3_0037.pdb_Y30Q__test_000769
+EEHEE_rd3_0037.pdb_Y30S__test_000771
+EEHEE_rd3_0037.pdb_Y30W__test_000774
+EEHEE_rd3_1498.pdb_A18E__test_000777
+EEHEE_rd3_1498.pdb_A18L__test_000783
+EEHEE_rd3_1498.pdb_A18M__test_000784
+EEHEE_rd3_1498.pdb_A18V__test_000791
+EEHEE_rd3_1498.pdb_A21F__test_000796
+EEHEE_rd3_1498.pdb_A21G__test_000797
+EEHEE_rd3_1498.pdb_A21K__test_000800
+EEHEE_rd3_1498.pdb_A21Q__test_000805
+EEHEE_rd3_1498.pdb_A22D__test_000812
+EEHEE_rd3_1498.pdb_A22H__test_000816
+EEHEE_rd3_1498.pdb_A22L__test_000819
+EEHEE_rd3_1498.pdb_A22T__test_000826
+EEHEE_rd3_1498.pdb_A26F__test_000832
+EEHEE_rd3_1498.pdb_A26K__test_000836
+EEHEE_rd3_1498.pdb_A26P__test_000840
+EEHEE_rd3_1498.pdb_A26Q__test_000841
+EEHEE_rd3_1498.pdb_A26R__test_000842
+EEHEE_rd3_1498.pdb_A26S__test_000843
+EEHEE_rd3_1498.pdb_E16L__test_000855
+EEHEE_rd3_1498.pdb_E16W__test_000864
+EEHEE_rd3_1498.pdb_E32M__test_000874
+EEHEE_rd3_1498.pdb_F25K__test_000890
+EEHEE_rd3_1498.pdb_F25T__test_000898
+EEHEE_rd3_1498.pdb_F25W__test_000900
+EEHEE_rd3_1498.pdb_F25Y__test_000901
+EEHEE_rd3_1498.pdb_G1A__test_000902
+EEHEE_rd3_1498.pdb_G1E__test_000904
+EEHEE_rd3_1498.pdb_G1R__test_000914
+EEHEE_rd3_1498.pdb_G1V__test_000917
+EEHEE_rd3_1498.pdb_G1Y__test_000919
+EEHEE_rd3_1498.pdb_G37E__test_000922
+EEHEE_rd3_1498.pdb_G37Y__test_000937
+EEHEE_rd3_1498.pdb_G7A__test_000938
+EEHEE_rd3_1498.pdb_G7H__test_000942
+EEHEE_rd3_1498.pdb_G7N__test_000947
+EEHEE_rd3_1498.pdb_G7W__test_000954
+EEHEE_rd3_1498.pdb_H36A__test_000956
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+EEHEE_rd3_1498.pdb_H36T__test_000970
+EEHEE_rd3_1498.pdb_H36W__test_000972
+EEHEE_rd3_1498.pdb_H41Y__test_000991
+EEHEE_rd3_1498.pdb_H43A__test_000992
+EEHEE_rd3_1498.pdb_H43I__test_000997
+EEHEE_rd3_1498.pdb_H43L__test_000999
+EEHEE_rd3_1498.pdb_H43S__test_001005
+EEHEE_rd3_1498.pdb_H4G__test_001014
+EEHEE_rd3_1498.pdb_H4I__test_001015
+EEHEE_rd3_1498.pdb_H4K__test_001016
+EEHEE_rd3_1498.pdb_H4L__test_001017
+EEHEE_rd3_1498.pdb_H4M__test_001018
+EEHEE_rd3_1498.pdb_H4P__test_001020
+EEHEE_rd3_1498.pdb_H4Q__test_001021
+EEHEE_rd3_1498.pdb_H4V__test_001025
+EEHEE_rd3_1498.pdb_I19A__test_001028
+EEHEE_rd3_1498.pdb_I19E__test_001030
+EEHEE_rd3_1498.pdb_I19F__test_001031
+EEHEE_rd3_1498.pdb_I19R__test_001040
+EEHEE_rd3_1498.pdb_K11D__test_001047
+EEHEE_rd3_1498.pdb_K11G__test_001050
+EEHEE_rd3_1498.pdb_K11P__test_001056
+EEHEE_rd3_1498.pdb_K11R__test_001058
+EEHEE_rd3_1498.pdb_K11T__test_001060
+EEHEE_rd3_1498.pdb_K17D__test_001065
+EEHEE_rd3_1498.pdb_K17V__test_001079
+EEHEE_rd3_1498.pdb_K20A__test_001082
+EEHEE_rd3_1498.pdb_K20G__test_001086
+EEHEE_rd3_1498.pdb_K20M__test_001090
+EEHEE_rd3_1498.pdb_K20P__test_001092
+EEHEE_rd3_1498.pdb_K20T__test_001096
+EEHEE_rd3_1498.pdb_K20Y__test_001099
+EEHEE_rd3_1498.pdb_K23E__test_001102
+EEHEE_rd3_1498.pdb_K23F__test_001103
+EEHEE_rd3_1498.pdb_K23L__test_001107
+EEHEE_rd3_1498.pdb_K23M__test_001108
+EEHEE_rd3_1498.pdb_K23R__test_001112
+EEHEE_rd3_1498.pdb_K23T__test_001114
+EEHEE_rd3_1498.pdb_K23Y__test_001117
+EEHEE_rd3_1498.pdb_K24E__test_001120
+EEHEE_rd3_1498.pdb_K24I__test_001124
+EEHEE_rd3_1498.pdb_K24W__test_001134
+EEHEE_rd3_1498.pdb_K24Y__test_001135
+EEHEE_rd3_1498.pdb_K27M__test_001144
+EEHEE_rd3_1498.pdb_K27Q__test_001147
+EEHEE_rd3_1498.pdb_K28D__test_001155
+EEHEE_rd3_1498.pdb_K28E__test_001156
+EEHEE_rd3_1498.pdb_K28I__test_001160
+EEHEE_rd3_1498.pdb_K28Q__test_001165
+EEHEE_rd3_1498.pdb_K28R__test_001166
+EEHEE_rd3_1498.pdb_L15E__test_001174
+EEHEE_rd3_1498.pdb_L15N__test_001181
+EEHEE_rd3_1498.pdb_L15R__test_001184
+EEHEE_rd3_1498.pdb_L15T__test_001186
+EEHEE_rd3_1498.pdb_L15W__test_001188
+EEHEE_rd3_1498.pdb_L31D__test_001191
+EEHEE_rd3_1498.pdb_L31P__test_001200
+EEHEE_rd3_1498.pdb_L31V__test_001205
+EEHEE_rd3_1498.pdb_L5F__test_001229
+EEHEE_rd3_1498.pdb_L5H__test_001231
+EEHEE_rd3_1498.pdb_L5I__test_001232
+EEHEE_rd3_1498.pdb_L5K__test_001233
+EEHEE_rd3_1498.pdb_L5M__test_001234
+EEHEE_rd3_1498.pdb_L5S__test_001239
+EEHEE_rd3_1498.pdb_L5V__test_001241
+EEHEE_rd3_1498.pdb_L5W__test_001242
+EEHEE_rd3_1498.pdb_N30I__test_001250
+EEHEE_rd3_1498.pdb_N30S__test_001257
+EEHEE_rd3_1498.pdb_N30T__test_001258
+EEHEE_rd3_1498.pdb_N30W__test_001260
+EEHEE_rd3_1498.pdb_N30Y__test_001261
+EEHEE_rd3_1498.pdb_N38A__test_001262
+EEHEE_rd3_1498.pdb_N38P__test_001272
+EEHEE_rd3_1498.pdb_N38Q__test_001273
+EEHEE_rd3_1498.pdb_N6I__test_001286
+EEHEE_rd3_1498.pdb_N6M__test_001289
+EEHEE_rd3_1498.pdb_N6P__test_001290
+EEHEE_rd3_1498.pdb_N6R__test_001292
+EEHEE_rd3_1498.pdb_N6V__test_001295
+EEHEE_rd3_1498.pdb_N6W__test_001296
+EEHEE_rd3_1498.pdb_P13H__test_001303
+EEHEE_rd3_1498.pdb_P13K__test_001305
+EEHEE_rd3_1498.pdb_P13Q__test_001309
+EEHEE_rd3_1498.pdb_P13R__test_001310
+EEHEE_rd3_1498.pdb_P13T__test_001312
+EEHEE_rd3_1498.pdb_P13V__test_001313
+EEHEE_rd3_1498.pdb_P13W__test_001314
+EEHEE_rd3_1498.pdb_P13Y__test_001315
+EEHEE_rd3_1498.pdb_Q34F__test_001319
+EEHEE_rd3_1498.pdb_Q34H__test_001321
+EEHEE_rd3_1498.pdb_Q34I__test_001322
+EEHEE_rd3_1498.pdb_Q34Y__test_001333
+EEHEE_rd3_1498.pdb_S14D__test_001335
+EEHEE_rd3_1498.pdb_S14E__test_001336
+EEHEE_rd3_1498.pdb_S14H__test_001339
+EEHEE_rd3_1498.pdb_S14I__test_001340
+EEHEE_rd3_1498.pdb_S14P__test_001345
+EEHEE_rd3_1498.pdb_T2F__test_001355
+EEHEE_rd3_1498.pdb_T2G__test_001356
+EEHEE_rd3_1498.pdb_T2I__test_001358
+EEHEE_rd3_1498.pdb_T39F__test_001373
+EEHEE_rd3_1498.pdb_T39L__test_001378
+EEHEE_rd3_1498.pdb_T39N__test_001380
+EEHEE_rd3_1498.pdb_T39V__test_001385
+EEHEE_rd3_1498.pdb_T9E__test_001390
+EEHEE_rd3_1498.pdb_T9G__test_001392
+EEHEE_rd3_1498.pdb_T9H__test_001393
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diff --git a/extract/embeddings/stability/cdconv/ids_train.txt b/extract/embeddings/stability/cdconv/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
--- /dev/null
+++ b/extract/embeddings/stability/cdconv/ids_valid.txt
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diff --git a/extract/embeddings/stability/cdconv/meta.json b/extract/embeddings/stability/cdconv/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ca51d7902fbb7509bbdfeeede1beeacc4e8180e3
--- /dev/null
+++ b/extract/embeddings/stability/cdconv/meta.json
@@ -0,0 +1,39 @@
+{
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+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 255,
+  "max_abs": 0.23158501088619232
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0015725457924418151,
+  "rel_change_coord_swap": 0.011715242639183998,
+  "rel_change_seq_shuffle": 0.004441954893991351,
+  "rel_change_rigid_motion": 7.288991810128209e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/dimenet/ids_test.txt b/extract/embeddings/stability/dimenet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/dimenet/ids_test.txt
@@ -0,0 +1,3000 @@
+EEHEE_rd3_0037.pdb_A19G__test_000004
+EEHEE_rd3_0037.pdb_A19H__test_000005
+EEHEE_rd3_0037.pdb_A19I__test_000006
+EEHEE_rd3_0037.pdb_A19S__test_000014
+EEHEE_rd3_0037.pdb_A19T__test_000015
+EEHEE_rd3_0037.pdb_A19Y__test_000018
+EEHEE_rd3_0037.pdb_A20D__test_000019
+EEHEE_rd3_0037.pdb_A20G__test_000022
+EEHEE_rd3_0037.pdb_A20H__test_000023
+EEHEE_rd3_0037.pdb_A20M__test_000027
+EEHEE_rd3_0037.pdb_A20V__test_000034
+EEHEE_rd3_0037.pdb_A22G__test_000040
+EEHEE_rd3_0037.pdb_A22I__test_000042
+EEHEE_rd3_0037.pdb_A22L__test_000044
+EEHEE_rd3_0037.pdb_A23H__test_000059
+EEHEE_rd3_0037.pdb_A23K__test_000061
+EEHEE_rd3_0037.pdb_A23N__test_000064
+EEHEE_rd3_0037.pdb_A23P__test_000065
+EEHEE_rd3_0037.pdb_A23Y__test_000072
+EEHEE_rd3_0037.pdb_D29E__test_000074
+EEHEE_rd3_0037.pdb_D29Y__test_000090
+EEHEE_rd3_0037.pdb_E17W__test_000107
+EEHEE_rd3_0037.pdb_E17Y__test_000108
+EEHEE_rd3_0037.pdb_E31G__test_000112
+EEHEE_rd3_0037.pdb_E31I__test_000114
+EEHEE_rd3_0037.pdb_E31L__test_000116
+EEHEE_rd3_0037.pdb_E31N__test_000118
+EEHEE_rd3_0037.pdb_E31Q__test_000120
+EEHEE_rd3_0037.pdb_E31T__test_000123
+EEHEE_rd3_0037.pdb_E31V__test_000124
+EEHEE_rd3_0037.pdb_E31W__test_000125
+EEHEE_rd3_0037.pdb_E9I__test_000132
+EEHEE_rd3_0037.pdb_E9K__test_000133
+EEHEE_rd3_0037.pdb_E9W__test_000143
+EEHEE_rd3_0037.pdb_G36A__test_000145
+EEHEE_rd3_0037.pdb_G36I__test_000150
+EEHEE_rd3_0037.pdb_G36M__test_000153
+EEHEE_rd3_0037.pdb_G36R__test_000157
+EEHEE_rd3_0037.pdb_G7A__test_000163
+EEHEE_rd3_0037.pdb_G7E__test_000165
+EEHEE_rd3_0037.pdb_G7M__test_000171
+EEHEE_rd3_0037.pdb_G7P__test_000173
+EEHEE_rd3_0037.pdb_G7W__test_000179
+EEHEE_rd3_0037.pdb_H35I__test_000186
+EEHEE_rd3_0037.pdb_H35K__test_000187
+EEHEE_rd3_0037.pdb_H35P__test_000191
+EEHEE_rd3_0037.pdb_H35R__test_000193
+EEHEE_rd3_0037.pdb_H35S__test_000194
+EEHEE_rd3_0037.pdb_I34Y__test_000216
+EEHEE_rd3_0037.pdb_I3D__test_000218
+EEHEE_rd3_0037.pdb_I3E__test_000219
+EEHEE_rd3_0037.pdb_I3K__test_000223
+EEHEE_rd3_0037.pdb_I3M__test_000225
+EEHEE_rd3_0037.pdb_I3T__test_000231
+EEHEE_rd3_0037.pdb_K21F__test_000238
+EEHEE_rd3_0037.pdb_K21H__test_000240
+EEHEE_rd3_0037.pdb_K21Q__test_000246
+EEHEE_rd3_0037.pdb_K24A__test_000253
+EEHEE_rd3_0037.pdb_K24D__test_000254
+EEHEE_rd3_0037.pdb_K24G__test_000257
+EEHEE_rd3_0037.pdb_K24H__test_000258
+EEHEE_rd3_0037.pdb_K24W__test_000269
+EEHEE_rd3_0037.pdb_K25G__test_000275
+EEHEE_rd3_0037.pdb_K25V__test_000286
+EEHEE_rd3_0037.pdb_K40A__test_000289
+EEHEE_rd3_0037.pdb_K40D__test_000290
+EEHEE_rd3_0037.pdb_K40E__test_000291
+EEHEE_rd3_0037.pdb_K40I__test_000295
+EEHEE_rd3_0037.pdb_K40L__test_000296
+EEHEE_rd3_0037.pdb_K4E__test_000309
+EEHEE_rd3_0037.pdb_K4M__test_000315
+EEHEE_rd3_0037.pdb_K4P__test_000317
+EEHEE_rd3_0037.pdb_K4W__test_000323
+EEHEE_rd3_0037.pdb_L14H__test_000330
+EEHEE_rd3_0037.pdb_L14R__test_000337
+EEHEE_rd3_0037.pdb_L14V__test_000340
+EEHEE_rd3_0037.pdb_N37D__test_000344
+EEHEE_rd3_0037.pdb_N6A__test_000361
+EEHEE_rd3_0037.pdb_N6F__test_000364
+EEHEE_rd3_0037.pdb_N6G__test_000365
+EEHEE_rd3_0037.pdb_N6R__test_000373
+EEHEE_rd3_0037.pdb_N6Y__test_000378
+EEHEE_rd3_0037.pdb_P13D__test_000380
+EEHEE_rd3_0037.pdb_P13H__test_000384
+EEHEE_rd3_0037.pdb_P13M__test_000388
+EEHEE_rd3_0037.pdb_P13V__test_000394
+EEHEE_rd3_0037.pdb_P16L__test_000405
+EEHEE_rd3_0037.pdb_P16Q__test_000408
+EEHEE_rd3_0037.pdb_P16Y__test_000414
+EEHEE_rd3_0037.pdb_P28F__test_000418
+EEHEE_rd3_0037.pdb_P28I__test_000421
+EEHEE_rd3_0037.pdb_P28M__test_000424
+EEHEE_rd3_0037.pdb_P28Q__test_000426
+EEHEE_rd3_0037.pdb_P28S__test_000428
+EEHEE_rd3_0037.pdb_Q18P__test_000444
+EEHEE_rd3_0037.pdb_Q18T__test_000447
+EEHEE_rd3_0037.pdb_Q33A__test_000451
+EEHEE_rd3_0037.pdb_Q33E__test_000453
+EEHEE_rd3_0037.pdb_Q33H__test_000456
+EEHEE_rd3_0037.pdb_Q33L__test_000459
+EEHEE_rd3_0037.pdb_Q33S__test_000464
+EEHEE_rd3_0037.pdb_Q33W__test_000467
+EEHEE_rd3_0037.pdb_Q8A__test_000469
+EEHEE_rd3_0037.pdb_Q8D__test_000470
+EEHEE_rd3_0037.pdb_Q8F__test_000472
+EEHEE_rd3_0037.pdb_Q8M__test_000478
+EEHEE_rd3_0037.pdb_Q8R__test_000481
+EEHEE_rd3_0037.pdb_R26E__test_000489
+EEHEE_rd3_0037.pdb_R26G__test_000491
+EEHEE_rd3_0037.pdb_R43F__test_000508
+EEHEE_rd3_0037.pdb_R43P__test_000516
+EEHEE_rd3_0037.pdb_R43S__test_000518
+EEHEE_rd3_0037.pdb_S15D__test_000524
+EEHEE_rd3_0037.pdb_S15H__test_000528
+EEHEE_rd3_0037.pdb_S15N__test_000533
+EEHEE_rd3_0037.pdb_S15T__test_000537
+EEHEE_rd3_0037.pdb_T11G__test_000545
+EEHEE_rd3_0037.pdb_T11K__test_000548
+EEHEE_rd3_0037.pdb_T11M__test_000550
+EEHEE_rd3_0037.pdb_T11N__test_000551
+EEHEE_rd3_0037.pdb_T1A__test_000559
+EEHEE_rd3_0037.pdb_T1H__test_000564
+EEHEE_rd3_0037.pdb_T1P__test_000570
+EEHEE_rd3_0037.pdb_T2A__test_000577
+EEHEE_rd3_0037.pdb_T2F__test_000580
+EEHEE_rd3_0037.pdb_T2H__test_000582
+EEHEE_rd3_0037.pdb_T2K__test_000584
+EEHEE_rd3_0037.pdb_T2M__test_000586
+EEHEE_rd3_0037.pdb_T2N__test_000587
+EEHEE_rd3_0037.pdb_T2S__test_000591
+EEHEE_rd3_0037.pdb_T2V__test_000592
+EEHEE_rd3_0037.pdb_T38D__test_000596
+EEHEE_rd3_0037.pdb_T38G__test_000599
+EEHEE_rd3_0037.pdb_T38H__test_000600
+EEHEE_rd3_0037.pdb_T38R__test_000608
+EEHEE_rd3_0037.pdb_T38Y__test_000612
+EEHEE_rd3_0037.pdb_T42F__test_000616
+EEHEE_rd3_0037.pdb_T42K__test_000620
+EEHEE_rd3_0037.pdb_T42Q__test_000625
+EEHEE_rd3_0037.pdb_T42R__test_000626
+EEHEE_rd3_0037.pdb_T42S__test_000627
+EEHEE_rd3_0037.pdb_V12A__test_000631
+EEHEE_rd3_0037.pdb_V12E__test_000633
+EEHEE_rd3_0037.pdb_V12G__test_000635
+EEHEE_rd3_0037.pdb_V12H__test_000636
+EEHEE_rd3_0037.pdb_V12Y__test_000648
+EEHEE_rd3_0037.pdb_V32A__test_000649
+EEHEE_rd3_0037.pdb_V32E__test_000651
+EEHEE_rd3_0037.pdb_V32G__test_000653
+EEHEE_rd3_0037.pdb_V32H__test_000654
+EEHEE_rd3_0037.pdb_V32R__test_000662
+EEHEE_rd3_0037.pdb_V32T__test_000664
+EEHEE_rd3_0037.pdb_V39D__test_000668
+EEHEE_rd3_0037.pdb_V39Q__test_000679
+EEHEE_rd3_0037.pdb_V39T__test_000682
+EEHEE_rd3_0037.pdb_V39Y__test_000684
+EEHEE_rd3_0037.pdb_V41P__test_000696
+EEHEE_rd3_0037.pdb_V41Q__test_000697
+EEHEE_rd3_0037.pdb_V41S__test_000699
+EEHEE_rd3_0037.pdb_V41W__test_000701
+EEHEE_rd3_0037.pdb_V41Y__test_000702
+EEHEE_rd3_0037.pdb_V5D__test_000704
+EEHEE_rd3_0037.pdb_W27D__test_000722
+EEHEE_rd3_0037.pdb_W27K__test_000728
+EEHEE_rd3_0037.pdb_W27R__test_000734
+EEHEE_rd3_0037.pdb_W27Y__test_000738
+EEHEE_rd3_0037.pdb_Y10D__test_000740
+EEHEE_rd3_0037.pdb_Y10H__test_000744
+EEHEE_rd3_0037.pdb_Y10I__test_000745
+EEHEE_rd3_0037.pdb_Y10K__test_000746
+EEHEE_rd3_0037.pdb_Y10L__test_000747
+EEHEE_rd3_0037.pdb_Y30F__test_000760
+EEHEE_rd3_0037.pdb_Y30I__test_000763
+EEHEE_rd3_0037.pdb_Y30M__test_000766
+EEHEE_rd3_0037.pdb_Y30Q__test_000769
+EEHEE_rd3_0037.pdb_Y30S__test_000771
+EEHEE_rd3_0037.pdb_Y30W__test_000774
+EEHEE_rd3_1498.pdb_A18E__test_000777
+EEHEE_rd3_1498.pdb_A18L__test_000783
+EEHEE_rd3_1498.pdb_A18M__test_000784
+EEHEE_rd3_1498.pdb_A18V__test_000791
+EEHEE_rd3_1498.pdb_A21F__test_000796
+EEHEE_rd3_1498.pdb_A21G__test_000797
+EEHEE_rd3_1498.pdb_A21K__test_000800
+EEHEE_rd3_1498.pdb_A21Q__test_000805
+EEHEE_rd3_1498.pdb_A22D__test_000812
+EEHEE_rd3_1498.pdb_A22H__test_000816
+EEHEE_rd3_1498.pdb_A22L__test_000819
+EEHEE_rd3_1498.pdb_A22T__test_000826
+EEHEE_rd3_1498.pdb_A26F__test_000832
+EEHEE_rd3_1498.pdb_A26K__test_000836
+EEHEE_rd3_1498.pdb_A26P__test_000840
+EEHEE_rd3_1498.pdb_A26Q__test_000841
+EEHEE_rd3_1498.pdb_A26R__test_000842
+EEHEE_rd3_1498.pdb_A26S__test_000843
+EEHEE_rd3_1498.pdb_E16L__test_000855
+EEHEE_rd3_1498.pdb_E16W__test_000864
+EEHEE_rd3_1498.pdb_E32M__test_000874
+EEHEE_rd3_1498.pdb_F25K__test_000890
+EEHEE_rd3_1498.pdb_F25T__test_000898
+EEHEE_rd3_1498.pdb_F25W__test_000900
+EEHEE_rd3_1498.pdb_F25Y__test_000901
+EEHEE_rd3_1498.pdb_G1A__test_000902
+EEHEE_rd3_1498.pdb_G1E__test_000904
+EEHEE_rd3_1498.pdb_G1R__test_000914
+EEHEE_rd3_1498.pdb_G1V__test_000917
+EEHEE_rd3_1498.pdb_G1Y__test_000919
+EEHEE_rd3_1498.pdb_G37E__test_000922
+EEHEE_rd3_1498.pdb_G37Y__test_000937
+EEHEE_rd3_1498.pdb_G7A__test_000938
+EEHEE_rd3_1498.pdb_G7H__test_000942
+EEHEE_rd3_1498.pdb_G7N__test_000947
+EEHEE_rd3_1498.pdb_G7W__test_000954
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+EEHEE_rd3_1498.pdb_H36W__test_000972
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+EEHEE_rd3_1498.pdb_H43A__test_000992
+EEHEE_rd3_1498.pdb_H43I__test_000997
+EEHEE_rd3_1498.pdb_H43L__test_000999
+EEHEE_rd3_1498.pdb_H43S__test_001005
+EEHEE_rd3_1498.pdb_H4G__test_001014
+EEHEE_rd3_1498.pdb_H4I__test_001015
+EEHEE_rd3_1498.pdb_H4K__test_001016
+EEHEE_rd3_1498.pdb_H4L__test_001017
+EEHEE_rd3_1498.pdb_H4M__test_001018
+EEHEE_rd3_1498.pdb_H4P__test_001020
+EEHEE_rd3_1498.pdb_H4Q__test_001021
+EEHEE_rd3_1498.pdb_H4V__test_001025
+EEHEE_rd3_1498.pdb_I19A__test_001028
+EEHEE_rd3_1498.pdb_I19E__test_001030
+EEHEE_rd3_1498.pdb_I19F__test_001031
+EEHEE_rd3_1498.pdb_I19R__test_001040
+EEHEE_rd3_1498.pdb_K11D__test_001047
+EEHEE_rd3_1498.pdb_K11G__test_001050
+EEHEE_rd3_1498.pdb_K11P__test_001056
+EEHEE_rd3_1498.pdb_K11R__test_001058
+EEHEE_rd3_1498.pdb_K11T__test_001060
+EEHEE_rd3_1498.pdb_K17D__test_001065
+EEHEE_rd3_1498.pdb_K17V__test_001079
+EEHEE_rd3_1498.pdb_K20A__test_001082
+EEHEE_rd3_1498.pdb_K20G__test_001086
+EEHEE_rd3_1498.pdb_K20M__test_001090
+EEHEE_rd3_1498.pdb_K20P__test_001092
+EEHEE_rd3_1498.pdb_K20T__test_001096
+EEHEE_rd3_1498.pdb_K20Y__test_001099
+EEHEE_rd3_1498.pdb_K23E__test_001102
+EEHEE_rd3_1498.pdb_K23F__test_001103
+EEHEE_rd3_1498.pdb_K23L__test_001107
+EEHEE_rd3_1498.pdb_K23M__test_001108
+EEHEE_rd3_1498.pdb_K23R__test_001112
+EEHEE_rd3_1498.pdb_K23T__test_001114
+EEHEE_rd3_1498.pdb_K23Y__test_001117
+EEHEE_rd3_1498.pdb_K24E__test_001120
+EEHEE_rd3_1498.pdb_K24I__test_001124
+EEHEE_rd3_1498.pdb_K24W__test_001134
+EEHEE_rd3_1498.pdb_K24Y__test_001135
+EEHEE_rd3_1498.pdb_K27M__test_001144
+EEHEE_rd3_1498.pdb_K27Q__test_001147
+EEHEE_rd3_1498.pdb_K28D__test_001155
+EEHEE_rd3_1498.pdb_K28E__test_001156
+EEHEE_rd3_1498.pdb_K28I__test_001160
+EEHEE_rd3_1498.pdb_K28Q__test_001165
+EEHEE_rd3_1498.pdb_K28R__test_001166
+EEHEE_rd3_1498.pdb_L15E__test_001174
+EEHEE_rd3_1498.pdb_L15N__test_001181
+EEHEE_rd3_1498.pdb_L15R__test_001184
+EEHEE_rd3_1498.pdb_L15T__test_001186
+EEHEE_rd3_1498.pdb_L15W__test_001188
+EEHEE_rd3_1498.pdb_L31D__test_001191
+EEHEE_rd3_1498.pdb_L31P__test_001200
+EEHEE_rd3_1498.pdb_L31V__test_001205
+EEHEE_rd3_1498.pdb_L5F__test_001229
+EEHEE_rd3_1498.pdb_L5H__test_001231
+EEHEE_rd3_1498.pdb_L5I__test_001232
+EEHEE_rd3_1498.pdb_L5K__test_001233
+EEHEE_rd3_1498.pdb_L5M__test_001234
+EEHEE_rd3_1498.pdb_L5S__test_001239
+EEHEE_rd3_1498.pdb_L5V__test_001241
+EEHEE_rd3_1498.pdb_L5W__test_001242
+EEHEE_rd3_1498.pdb_N30I__test_001250
+EEHEE_rd3_1498.pdb_N30S__test_001257
+EEHEE_rd3_1498.pdb_N30T__test_001258
+EEHEE_rd3_1498.pdb_N30W__test_001260
+EEHEE_rd3_1498.pdb_N30Y__test_001261
+EEHEE_rd3_1498.pdb_N38A__test_001262
+EEHEE_rd3_1498.pdb_N38P__test_001272
+EEHEE_rd3_1498.pdb_N38Q__test_001273
+EEHEE_rd3_1498.pdb_N6I__test_001286
+EEHEE_rd3_1498.pdb_N6M__test_001289
+EEHEE_rd3_1498.pdb_N6P__test_001290
+EEHEE_rd3_1498.pdb_N6R__test_001292
+EEHEE_rd3_1498.pdb_N6V__test_001295
+EEHEE_rd3_1498.pdb_N6W__test_001296
+EEHEE_rd3_1498.pdb_P13H__test_001303
+EEHEE_rd3_1498.pdb_P13K__test_001305
+EEHEE_rd3_1498.pdb_P13Q__test_001309
+EEHEE_rd3_1498.pdb_P13R__test_001310
+EEHEE_rd3_1498.pdb_P13T__test_001312
+EEHEE_rd3_1498.pdb_P13V__test_001313
+EEHEE_rd3_1498.pdb_P13W__test_001314
+EEHEE_rd3_1498.pdb_P13Y__test_001315
+EEHEE_rd3_1498.pdb_Q34F__test_001319
+EEHEE_rd3_1498.pdb_Q34H__test_001321
+EEHEE_rd3_1498.pdb_Q34I__test_001322
+EEHEE_rd3_1498.pdb_Q34Y__test_001333
+EEHEE_rd3_1498.pdb_S14D__test_001335
+EEHEE_rd3_1498.pdb_S14E__test_001336
+EEHEE_rd3_1498.pdb_S14H__test_001339
+EEHEE_rd3_1498.pdb_S14I__test_001340
+EEHEE_rd3_1498.pdb_S14P__test_001345
+EEHEE_rd3_1498.pdb_T2F__test_001355
+EEHEE_rd3_1498.pdb_T2G__test_001356
+EEHEE_rd3_1498.pdb_T2I__test_001358
+EEHEE_rd3_1498.pdb_T39F__test_001373
+EEHEE_rd3_1498.pdb_T39L__test_001378
+EEHEE_rd3_1498.pdb_T39N__test_001380
+EEHEE_rd3_1498.pdb_T39V__test_001385
+EEHEE_rd3_1498.pdb_T9E__test_001390
+EEHEE_rd3_1498.pdb_T9G__test_001392
+EEHEE_rd3_1498.pdb_T9H__test_001393
+EEHEE_rd3_1498.pdb_T9M__test_001397
+EEHEE_rd3_1498.pdb_T9N__test_001398
+EEHEE_rd3_1498.pdb_T9V__test_001403
+EEHEE_rd3_1498.pdb_V10E__test_001408
+EEHEE_rd3_1498.pdb_V10K__test_001413
+EEHEE_rd3_1498.pdb_V10M__test_001415
+EEHEE_rd3_1498.pdb_V12A__test_001424
+EEHEE_rd3_1498.pdb_V12D__test_001425
+EEHEE_rd3_1498.pdb_V12W__test_001440
+EEHEE_rd3_1498.pdb_V33I__test_001448
+EEHEE_rd3_1498.pdb_V33M__test_001451
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/dimenet/meta.json b/extract/embeddings/stability/dimenet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0f7936df73f52ec984c249e1b5d0218b29991dec
--- /dev/null
+++ b/extract/embeddings/stability/dimenet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "dimenet",
+ "family": "registry",
+ "target": "dimenet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "71e5f811f644cdf2",
+ "n_parameters": 362752,
+ "task": "stability",
+ "date": "2026-09-19 18:48",
+ "seconds": 71.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.257164478302002
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.00359466125781171,
+  "rel_change_coord_swap": 0.005332541273893109,
+  "rel_change_seq_shuffle": 0.01124036381104809,
+  "rel_change_rigid_motion": 1.23831448402748e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm1b/ids_test.txt b/extract/embeddings/stability/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm1b/ids_test.txt
@@ -0,0 +1,3000 @@
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm1b/meta.json b/extract/embeddings/stability/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a350e94c37bd6374d80d7662e2f85c9c416ff267
--- /dev/null
+++ b/extract/embeddings/stability/esm1b/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm1b",
+ "family": "hf_plm",
+ "target": "facebook/esm1b_t33_650M_UR50S",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm1b_t33_650M_UR50S",
+ "checkpoint_revision": "7b37824baec4d3658e1df7479222a7c79b465b76",
+ "dtype": "float32",
+ "hidden_size": 1280,
+ "n_layers": 33,
+ "n_parameters": 650716821,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:49",
+ "seconds": 34.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 17.899150848388672
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.11968619571511047,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm2_150m/ids_test.txt b/extract/embeddings/stability/esm2_150m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_150m/ids_test.txt
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm2_150m/meta.json b/extract/embeddings/stability/esm2_150m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..eb46faa7b462ec4941c4e7c3cf1058498121cc75
--- /dev/null
+++ b/extract/embeddings/stability/esm2_150m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_150m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t30_150M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t30_150M_UR50D",
+ "checkpoint_revision": "a695f6045e2e32885fa60af20c13cb35398ce30c",
+ "dtype": "float32",
+ "hidden_size": 640,
+ "n_layers": 30,
+ "n_parameters": 148385241,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:43",
+ "seconds": 11.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 640,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 639,
+  "max_abs": 7.328146934509277
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.23306057014528236,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm2_35m/ids_test.txt b/extract/embeddings/stability/esm2_35m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_35m/ids_test.txt
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm2_35m/meta.json b/extract/embeddings/stability/esm2_35m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a89c94fbb1c41a196e36f5fd5f0c4ae693794785
--- /dev/null
+++ b/extract/embeddings/stability/esm2_35m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_35m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t12_35M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t12_35M_UR50D",
+ "checkpoint_revision": "6fbf070e65b0b7291e7bbcd451118c216cff79d8",
+ "dtype": "float32",
+ "hidden_size": 480,
+ "n_layers": 12,
+ "n_parameters": 33762001,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:43",
+ "seconds": 6.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 480,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 479,
+  "max_abs": 6.426964282989502
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.2002921266035882,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm2_3b/ids_test.txt b/extract/embeddings/stability/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_3b/ids_test.txt
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm2_3b/meta.json b/extract/embeddings/stability/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..52ac47ffb4d9f8c8c7ab6741bd398a145d84aede
--- /dev/null
+++ b/extract/embeddings/stability/esm2_3b/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_3b",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t36_3B_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues; fp16 weights",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t36_3B_UR50D",
+ "checkpoint_revision": "476b639933c8baad5ad09a60ac1a87f987b656fc",
+ "dtype": "float16",
+ "hidden_size": 2560,
+ "n_layers": 36,
+ "n_parameters": 2835070881,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 19:55",
+ "seconds": 40.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 2560,
+  "max_abs": 14.533437728881836
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.16059037802733606,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm2_650m/ids_test.txt b/extract/embeddings/stability/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_650m/ids_test.txt
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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diff --git a/extract/embeddings/stability/esm2_650m/ids_valid.txt b/extract/embeddings/stability/esm2_650m/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm2_650m/meta.json b/extract/embeddings/stability/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..08b16caf484d28e7ea42d06c9f1eca5010231c3e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_650m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_650m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t33_650M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t33_650M_UR50D",
+ "checkpoint_revision": "08e4846e537177426273712802403f7ba8261b6c",
+ "dtype": "float32",
+ "hidden_size": 1280,
+ "n_layers": 33,
+ "n_parameters": 650714261,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:45",
+ "seconds": 34.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 8.887693405151367
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.18661678857220632,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm2_8m/ids_test.txt b/extract/embeddings/stability/esm2_8m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_8m/ids_test.txt
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diff --git a/extract/embeddings/stability/esm2_8m/ids_train.txt b/extract/embeddings/stability/esm2_8m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/esm2_8m/ids_train.txt
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diff --git a/extract/embeddings/stability/esm2_8m/ids_valid.txt b/extract/embeddings/stability/esm2_8m/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm2_8m/meta.json b/extract/embeddings/stability/esm2_8m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..35f2d3eab0da3aabc557aba46798384b64d9f16e
--- /dev/null
+++ b/extract/embeddings/stability/esm2_8m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_8m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t6_8M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t6_8M_UR50D",
+ "checkpoint_revision": "c731040fcd8d73dceaa04b0a8e6329b345b0f5df",
+ "dtype": "float32",
+ "hidden_size": 320,
+ "n_layers": 6,
+ "n_parameters": 7737401,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:42",
+ "seconds": 3.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 320,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 319,
+  "max_abs": 5.3706135749816895
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.2041863371369027,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/esm3/ids_test.txt b/extract/embeddings/stability/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/esm3/ids_test.txt
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diff --git a/extract/embeddings/stability/esm3/ids_train.txt b/extract/embeddings/stability/esm3/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/esm3/ids_train.txt
@@ -0,0 +1,6000 @@
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm3/meta.json b/extract/embeddings/stability/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3005af121ecb7faa087d5f1134f5d613333ecd82
--- /dev/null
+++ b/extract/embeddings/stability/esm3/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "esm3",
+ "family": "patched",
+ "target": "esm3_inproc",
+ "weights": "pretrained",
+ "rule": "final trunk residue embeddings, sequence and structure tracks",
+ "env": "base",
+ "checkpoint": "esm3-sm-open-v1/data/weights/esm3_sm_open_v1.pth",
+ "dtype": "bfloat16",
+ "n_parameters": 1401735748,
+ "inputs_passed": "sequence track: true residues; structure track: VQ-VAE tokens from the real backbone (N, CA, C, O, CB) plus coordinates for geometric attention; function, SASA and secondary-structure tracks at their defaults",
+ "patch": "patched/esm3_inproc.py",
+ "task": "stability",
+ "date": "2026-09-19 20:25",
+ "seconds": 260.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1536,
+  "max_abs": 8692.8369140625
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.3911045424821484,
+  "rel_change_coord_swap": 0.1052052461015038,
+  "rel_change_seq_shuffle": 0.23244728451209695,
+  "rel_change_rigid_motion": 0.0020265780064980155,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/stability/esm_if1/ids_test.txt b/extract/embeddings/stability/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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diff --git a/extract/embeddings/stability/esm_if1/ids_train.txt b/extract/embeddings/stability/esm_if1/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/esm_if1/ids_train.txt
@@ -0,0 +1,6000 @@
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/esm_if1/meta.json b/extract/embeddings/stability/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4608b130fc566008cdea7870c2aad060b5e01ec5
--- /dev/null
+++ b/extract/embeddings/stability/esm_if1/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "esm_if1",
+ "family": "registry",
+ "target": "esm_if",
+ "weights": "pretrained",
+ "rule": "GVP-Transformer encoder output before decoding",
+ "env": "base",
+ "weights_sha256": "0edb76de890a0108",
+ "n_parameters": 141662150,
+ "task": "stability",
+ "date": "2026-09-19 19:32",
+ "seconds": 390.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 511,
+  "max_abs": 1.1583638191223145
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038824098366321,
+  "rel_change_coord_swap": 0.4455433958503876,
+  "rel_change_seq_shuffle": 3.7498057269072577e-07,
+  "rel_change_rigid_motion": 1.1009514245534706e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/foldseek_3di/ids_test.txt b/extract/embeddings/stability/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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diff --git a/extract/embeddings/stability/foldseek_3di/ids_train.txt b/extract/embeddings/stability/foldseek_3di/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/foldseek_3di/ids_train.txt
@@ -0,0 +1,6000 @@
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/foldseek_3di/meta.json b/extract/embeddings/stability/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5809db69db46869569f488022d8cf1f21a7c72a8
--- /dev/null
+++ b/extract/embeddings/stability/foldseek_3di/meta.json
@@ -0,0 +1,40 @@
+{
+ "encoder": "foldseek_3di",
+ "family": "patched",
+ "target": "foldseek_3di",
+ "weights": "pretrained",
+ "rule": "one-hot 3Di state per residue; protein level is the state frequency",
+ "env": "base",
+ "tool": "mini3di 0.2.1",
+ "inputs_passed": "N, CA, C, CB coordinates",
+ "n_parameters": 0,
+ "patch": "patched/foldseek_3di.py",
+ "task": "stability",
+ "date": "2026-09-19 19:26",
+ "seconds": 5.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 7952,
+  "numerical_rank": 19,
+  "max_abs": 0.9599999785423279
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.7178714286952135,
+  "rel_change_coord_swap": 0.49931369393859204,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/foldvision/ids_test.txt b/extract/embeddings/stability/foldvision/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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diff --git a/extract/embeddings/stability/foldvision/ids_train.txt b/extract/embeddings/stability/foldvision/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/foldvision/ids_train.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/foldvision/meta.json b/extract/embeddings/stability/foldvision/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e2a46334cdb8251fbe010a8d299fe82071d1a6e4
--- /dev/null
+++ b/extract/embeddings/stability/foldvision/meta.json
@@ -0,0 +1,42 @@
+{
+ "encoder": "foldvision",
+ "family": "patched",
+ "target": "foldvision_global",
+ "weights": "pretrained",
+ "rule": "native FoldVisionEncoder.encode global embedding; no residue states",
+ "env": "base",
+ "checkpoint": "AlexanderKroll/foldvision-encoder",
+ "n_parameters": 122226304,
+ "inputs_passed": "the structure file as given (all atoms present in it), voxelised by FoldVision's own preprocessing",
+ "patch": "patched/foldvision_global.py",
+ "residue_level": false,
+ "pose": "principal-axis pose with fixed axis signs, applied to the structure file before voxelisation",
+ "task": "stability",
+ "date": "2026-09-19 18:58",
+ "seconds": 621.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 4.543148040771484
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.9399117827415466,
+  "rel_change_coord_swap": 0.19160349667072296,
+  "rel_change_seq_shuffle": 0.029323811642825603,
+  "rel_change_rigid_motion": 0.0002744854864431545,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/gcpnet_pretrained/ids_test.txt b/extract/embeddings/stability/gcpnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/gcpnet_pretrained/ids_test.txt
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diff --git a/extract/embeddings/stability/gcpnet_pretrained/ids_train.txt b/extract/embeddings/stability/gcpnet_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/gcpnet_pretrained/ids_train.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/gcpnet_pretrained/meta.json b/extract/embeddings/stability/gcpnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..21d6176c294e5aabaa3805c6cc4ab3d6fb6548f9
--- /dev/null
+++ b/extract/embeddings/stability/gcpnet_pretrained/meta.json
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+{
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+ "family": "patched",
+ "target": "gcpnet_official",
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+ "rule": "official PSR model; 100 scalar channels + 16 vector norms, mean over the heavy atoms of each residue",
+ "env": "base",
+ "checkpoint": "external_repos/GCPNet/checkpoints/PSR/model_epoch_115_localpearson_0_616_localspearman_0_532_localkendall_0_385_globalpearson_0_871_globalspearman_0_869_globalkendall_0_676.ckpt",
+ "checkpoint_sha256": "ff7b73be01fb57d5",
+ "checkpoint_loaded_by": "strict=True",
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+ "inputs_passed": "all heavy atoms of the structure file (elements and coordinates); residue identity enters through side-chain atoms",
+ "patch": "patched/gcpnet_official.py",
+ "task": "stability",
+ "date": "2026-09-19 20:26",
+ "seconds": 474.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
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+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
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+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
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+  "rel_change_seq_shuffle": 0.03569233790040016,
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+  "verdict": "pass"
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diff --git a/extract/embeddings/stability/gcpnet_random/ids_test.txt b/extract/embeddings/stability/gcpnet_random/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
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diff --git a/extract/embeddings/stability/gcpnet_random/ids_train.txt b/extract/embeddings/stability/gcpnet_random/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/gcpnet_random/ids_train.txt
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diff --git a/extract/embeddings/stability/gcpnet_random/ids_valid.txt b/extract/embeddings/stability/gcpnet_random/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/gcpnet_random/meta.json b/extract/embeddings/stability/gcpnet_random/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7da4965a09f8fee80c6f1a83364a97585cf9602d
--- /dev/null
+++ b/extract/embeddings/stability/gcpnet_random/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "gcpnet_random",
+ "family": "patched",
+ "target": "gcpnet_official_random",
+ "weights": "random",
+ "rule": "official architecture, random weights; 100 scalar channels + 16 vector norms per residue",
+ "env": "base",
+ "checkpoint": null,
+ "checkpoint_sha256": null,
+ "checkpoint_loaded_by": "none (random weights, fixed seed)",
+ "weights_sha256": "cdec9adf86f7cd39",
+ "n_parameters": 1153181,
+ "inputs_passed": "all heavy atoms of the structure file (elements and coordinates); residue identity enters through side-chain atoms",
+ "patch": "patched/gcpnet_official.py",
+ "task": "stability",
+ "date": "2026-09-19 20:04",
+ "seconds": 495.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 116,
+  "max_abs": 2.1213066577911377
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.06854107603430748,
+  "rel_change_coord_swap": 0.005355736706405878,
+  "rel_change_seq_shuffle": 0.0014150030328892171,
+  "rel_change_rigid_motion": 1.3333194146980532e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/gearnet/ids_test.txt b/extract/embeddings/stability/gearnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/gearnet/ids_test.txt
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/gearnet/ids_train.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/gearnet/meta.json b/extract/embeddings/stability/gearnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4693881625ae03ce4e5935897b176e69e38e95a4
--- /dev/null
+++ b/extract/embeddings/stability/gearnet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet",
+ "family": "registry",
+ "target": "gearnet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "c0af89eafe340139",
+ "n_parameters": 6641408,
+ "task": "stability",
+ "date": "2026-09-19 18:55",
+ "seconds": 81.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 511,
+  "max_abs": 3.520357131958008
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.05966170943530161,
+  "rel_change_coord_swap": 0.0903857713791805,
+  "rel_change_seq_shuffle": 0.2058370455057908,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/gearnet_pretrained/ids_test.txt b/extract/embeddings/stability/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..4b96d74daea560598990a125d05a72be01f44550
--- /dev/null
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+{
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+ "task": "stability",
+ "date": "2026-09-19 20:17",
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+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
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+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
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+  "verdict": "pass"
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diff --git a/extract/embeddings/stability/gvp/ids_test.txt b/extract/embeddings/stability/gvp/ids_test.txt
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index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/gvp/ids_train.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/gvp/meta.json b/extract/embeddings/stability/gvp/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c6dfbd45f019701b75f6ef21e4342eb9471e062f
--- /dev/null
+++ b/extract/embeddings/stability/gvp/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "gvp",
+ "family": "patched",
+ "target": "gvp_inproc",
+ "weights": "random",
+ "rule": "scalar channels + vector norms (invariant), masked mean",
+ "env": "base",
+ "weights_sha256": "4199962f00f771e2",
+ "seed": 20260919,
+ "n_parameters": 476935,
+ "inputs_passed": "backbone coordinates and residue identity",
+ "patch": "patched/gvp_inproc.py",
+ "task": "stability",
+ "date": "2026-09-19 19:00",
+ "seconds": 90.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 115,
+  "max_abs": 2.8747527599334717
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.031185454351663002,
+  "rel_change_coord_swap": 0.006320141648041101,
+  "rel_change_seq_shuffle": 0.0027774650952451995,
+  "rel_change_rigid_motion": 8.275581229078682e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/ipa/ids_test.txt b/extract/embeddings/stability/ipa/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/ipa/ids_train.txt
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diff --git a/extract/embeddings/stability/ipa/ids_valid.txt b/extract/embeddings/stability/ipa/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/ipa/meta.json b/extract/embeddings/stability/ipa/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..09395b369d7d2f8a1d029019ffae6fcdb7597b9d
--- /dev/null
+++ b/extract/embeddings/stability/ipa/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa",
+ "family": "registry",
+ "target": "ipa",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "e78c71b9309a3464",
+ "n_parameters": 648016,
+ "task": "stability",
+ "date": "2026-09-19 19:06",
+ "seconds": 183.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.6402500867843628
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.12257405052335979,
+  "rel_change_coord_swap": 0.051555149433614486,
+  "rel_change_seq_shuffle": 0.0797983256679259,
+  "rel_change_rigid_motion": 3.342620076301104e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/ipa_pretrained/ids_test.txt b/extract/embeddings/stability/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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new file mode 100644
index 0000000000000000000000000000000000000000..bc15519fe5972a3f19ee8149160cc928a9d9c977
--- /dev/null
+++ b/extract/embeddings/stability/ipa_pretrained/meta.json
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+{
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+ "env": "base",
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+ "task": "stability",
+ "date": "2026-09-19 20:18",
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+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
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+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
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+  "rel_change_rigid_motion": 4.298113087293277e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/stability/mace/ids_test.txt b/extract/embeddings/stability/mace/ids_test.txt
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index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
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diff --git a/extract/embeddings/stability/mace/ids_train.txt b/extract/embeddings/stability/mace/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
+++ b/extract/embeddings/stability/mace/ids_train.txt
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diff --git a/extract/embeddings/stability/mace/ids_valid.txt b/extract/embeddings/stability/mace/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/mace/meta.json b/extract/embeddings/stability/mace/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6755cd685bf61c6c7fa47c2764fc596e0b7c6606
--- /dev/null
+++ b/extract/embeddings/stability/mace/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "mace",
+ "family": "registry",
+ "target": "mace",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "e8e9d6fd9722cc4e",
+ "n_parameters": 584064,
+ "task": "stability",
+ "date": "2026-09-19 18:52",
+ "seconds": 124.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.1428099870681763
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.014915865242322838,
+  "rel_change_coord_swap": 0.05683945173750876,
+  "rel_change_seq_shuffle": 0.0523291422188011,
+  "rel_change_rigid_motion": 1.3602486243731065e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/pottsmpnn/ids_test.txt b/extract/embeddings/stability/pottsmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/pottsmpnn/meta.json b/extract/embeddings/stability/pottsmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..bdffc6d9b9c0ec1b147ce9456ede7f585a6c4987
--- /dev/null
+++ b/extract/embeddings/stability/pottsmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "pottsmpnn",
+ "family": "registry",
+ "target": "pottsmpnn",
+ "weights": "random",
+ "rule": "encoder h_V after 3 layers, masked mean",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "fd9636d73a1e9994",
+ "n_parameters": 1712085,
+ "task": "stability",
+ "date": "2026-09-19 19:14",
+ "seconds": 207.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 3.0391757488250732
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.07189607480629943,
+  "rel_change_coord_swap": 0.06452992568345384,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.150863828075338e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/pottsmpnn_ft/ids_test.txt b/extract/embeddings/stability/pottsmpnn_ft/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
+++ b/extract/embeddings/stability/pottsmpnn_ft/ids_test.txt
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diff --git a/extract/embeddings/stability/pottsmpnn_ft/ids_train.txt b/extract/embeddings/stability/pottsmpnn_ft/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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diff --git a/extract/embeddings/stability/pottsmpnn_ft/ids_valid.txt b/extract/embeddings/stability/pottsmpnn_ft/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/pottsmpnn_ft/meta.json b/extract/embeddings/stability/pottsmpnn_ft/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..8eb3f4f9367f7330313d68f3a25c949f321ebfd6
--- /dev/null
+++ b/extract/embeddings/stability/pottsmpnn_ft/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_ft",
+ "family": "registry",
+ "target": "pottsmpnn_ft_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "b8171c21b2e3eab7",
+ "n_parameters": 1712085,
+ "task": "stability",
+ "date": "2026-09-19 20:05",
+ "seconds": 30.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.611365795135498
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.5082692283690026,
+  "rel_change_coord_swap": 0.13421373340726975,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.330835728765909e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/pottsmpnn_pretrained/ids_test.txt b/extract/embeddings/stability/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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diff --git a/extract/embeddings/stability/pottsmpnn_pretrained/ids_train.txt b/extract/embeddings/stability/pottsmpnn_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/pottsmpnn_pretrained/meta.json b/extract/embeddings/stability/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1fc2a8602f7d05618f68092f667fe1e339acd7a1
--- /dev/null
+++ b/extract/embeddings/stability/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_pretrained",
+ "family": "registry",
+ "target": "pottsmpnn_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "1cfd2bd3bed04f09",
+ "n_parameters": 1712085,
+ "task": "stability",
+ "date": "2026-09-19 20:04",
+ "seconds": 31.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 3.3392980098724365
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6454550569687352,
+  "rel_change_coord_swap": 0.12076814557594767,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.1436842851380084e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/pottsmpnn_soluble/ids_test.txt b/extract/embeddings/stability/pottsmpnn_soluble/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
--- /dev/null
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diff --git a/extract/embeddings/stability/pottsmpnn_soluble/ids_valid.txt b/extract/embeddings/stability/pottsmpnn_soluble/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/pottsmpnn_soluble/meta.json b/extract/embeddings/stability/pottsmpnn_soluble/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..be54d07ab59f453e9f1241475fda035190199e85
--- /dev/null
+++ b/extract/embeddings/stability/pottsmpnn_soluble/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_soluble",
+ "family": "registry",
+ "target": "pottsmpnn_soluble_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "31f0aac7f4cefa1a",
+ "n_parameters": 1712085,
+ "task": "stability",
+ "date": "2026-09-19 20:05",
+ "seconds": 30.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.0290579795837402
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6675711994212048,
+  "rel_change_coord_swap": 0.17917227338286784,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.4140547445011483e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/prostt5/ids_test.txt b/extract/embeddings/stability/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/prostt5/meta.json b/extract/embeddings/stability/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..36e441b1dfc6b4be536c47f778d07c40171e09e8
--- /dev/null
+++ b/extract/embeddings/stability/prostt5/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "prostt5",
+ "family": "hf_plm",
+ "target": "Rostlab/ProstT5",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues; amino-acid track with the <AA2fold> prefix, no 3Di input",
+ "env": "base",
+ "checkpoint": "Rostlab/ProstT5",
+ "checkpoint_revision": "d7d097d5bf9a993ab8f68488b4681d6ca70db9e5",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208164352,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 19:04",
+ "seconds": 56.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 1.3276084661483765
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.5110924480134234,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/protbert_bfd/ids_test.txt b/extract/embeddings/stability/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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diff --git a/extract/embeddings/stability/protbert_bfd/ids_valid.txt b/extract/embeddings/stability/protbert_bfd/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/protbert_bfd/meta.json b/extract/embeddings/stability/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9a18fd0db293dfb4f1535d9e68f5475d2b92acfb
--- /dev/null
+++ b/extract/embeddings/stability/protbert_bfd/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "protbert_bfd",
+ "family": "hf_plm",
+ "target": "Rostlab/prot_bert_bfd",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "Rostlab/prot_bert_bfd",
+ "checkpoint_revision": "6c5c8a55a52ff08a664dfd584aa1773f125a0487",
+ "dtype": "float32",
+ "hidden_size": 1024,
+ "n_layers": 30,
+ "n_parameters": 418881536,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:52",
+ "seconds": 18.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1023,
+  "max_abs": 1.9042028188705444
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.4072423163663681,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/proteinmpnn/ids_test.txt b/extract/embeddings/stability/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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new file mode 100644
index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/proteinmpnn/meta.json b/extract/embeddings/stability/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a918c2f5e4aa20b4d41fe4bb3927b73a519c01df
--- /dev/null
+++ b/extract/embeddings/stability/proteinmpnn/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "proteinmpnn",
+ "family": "registry",
+ "target": "proteinmpnn_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V after 3 encoder layers, before the decoder",
+ "env": "base",
+ "checkpoint": "checkpoints/proteinmpnn_v48_020.pt",
+ "checkpoint_sha256": "c9cb4a671d796041",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "01d6f9d31117f274",
+ "n_parameters": 1660485,
+ "task": "stability",
+ "date": "2026-09-19 19:22",
+ "seconds": 215.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.2289862632751465
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+ "input_audit": {
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+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/stability/prottrans_t5_xl_u50/ids_test.txt b/extract/embeddings/stability/prottrans_t5_xl_u50/ids_test.txt
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index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/prottrans_t5_xl_u50/meta.json b/extract/embeddings/stability/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..de47277aba1c7036bd4599e32a63ed9e95adf707
--- /dev/null
+++ b/extract/embeddings/stability/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "prottrans_t5_xl_u50",
+ "family": "hf_plm",
+ "target": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "checkpoint_revision": "94a6abc029ae13029317b140b7424e012bf8dfbf",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208141824,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "stability",
+ "date": "2026-09-19 18:59",
+ "seconds": 41.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 0.6220409870147705
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.7503630666663541,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/ref_composition/ids_test.txt b/extract/embeddings/stability/ref_composition/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/ref_composition/meta.json b/extract/embeddings/stability/ref_composition/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a5a22d096cd61aafb6c960b04acd6f70381654ad
--- /dev/null
+++ b/extract/embeddings/stability/ref_composition/meta.json
@@ -0,0 +1,18 @@
+{
+ "encoder": "ref_composition",
+ "family": "non-learned reference",
+ "weights": "none",
+ "n_parameters": 0,
+ "rule": "20 amino-acid frequencies, log length, length/600, fraction outside the 20-letter alphabet",
+ "inputs_passed": "amino-acid sequence only",
+ "hidden_size": 23,
+ "task": "stability",
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+ "n_per_split": {
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+  "valid": 1500,
+  "test": 3000
+ },
+ "purpose": "downstream floor: what the task scores without any learned representation",
+ "date": "2026-09-21 14:00"
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/saprot/ids_test.txt b/extract/embeddings/stability/saprot/ids_test.txt
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index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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new file mode 100644
index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/saprot/meta.json b/extract/embeddings/stability/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1fcdc8cef372228e42dae479f49372d63cb79bff
--- /dev/null
+++ b/extract/embeddings/stability/saprot/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "saprot",
+ "family": "patched",
+ "target": "saprot_hf",
+ "weights": "pretrained",
+ "rule": "final hidden states at the L residue positions of AA+3Di tokens",
+ "env": "base",
+ "checkpoint": "westlake-repl/SaProt_650M_AF2",
+ "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38",
+ "n_parameters": 651242901,
+ "inputs_passed": "amino-acid track: real sequence; 3Di track: real tokens from mini3di on the structure; no pLDDT masking",
+ "patch": "patched/saprot_hf.py",
+ "task": "stability",
+ "date": "2026-09-19 19:14",
+ "seconds": 372.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 1.7069497108459473
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.8705030813272382,
+  "rel_change_coord_swap": 0.4102216970171252,
+  "rel_change_seq_shuffle": 0.8413755808217256,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/schnet/ids_test.txt b/extract/embeddings/stability/schnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/schnet/meta.json b/extract/embeddings/stability/schnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c1784edd2b0f5fa4d9c07622ee521f162a295a7d
--- /dev/null
+++ b/extract/embeddings/stability/schnet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "schnet",
+ "family": "registry",
+ "target": "schnet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "a554781da0916f60",
+ "n_parameters": 244480,
+ "task": "stability",
+ "date": "2026-09-19 18:43",
+ "seconds": 20.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.1597294807434082
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.024272346150889114,
+  "rel_change_coord_swap": 0.04067997024144254,
+  "rel_change_seq_shuffle": 0.0926744111105295,
+  "rel_change_rigid_motion": 1.4309623780125316e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/tfn/ids_test.txt b/extract/embeddings/stability/tfn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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new file mode 100644
index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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diff --git a/extract/embeddings/stability/tfn/ids_valid.txt b/extract/embeddings/stability/tfn/ids_valid.txt
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index 0000000000000000000000000000000000000000..9e907c3b5e7d33c867ff6dd765d0cbb6e7c72ee0
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diff --git a/extract/embeddings/stability/tfn/meta.json b/extract/embeddings/stability/tfn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2950c30009144fb53583e4897acae67b61c4f59e
--- /dev/null
+++ b/extract/embeddings/stability/tfn/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "tfn",
+ "family": "registry",
+ "target": "tfn",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "b07ce6d9887ef8db",
+ "n_parameters": 250880,
+ "task": "stability",
+ "date": "2026-09-19 18:45",
+ "seconds": 82.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 4.088077545166016
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03591847389124728,
+  "rel_change_coord_swap": 0.08890222001118514,
+  "rel_change_seq_shuffle": 0.15717389464953313,
+  "rel_change_rigid_motion": 1.055602025398984e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/stability/tfn_pretrained/ids_test.txt b/extract/embeddings/stability/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e
--- /dev/null
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index 0000000000000000000000000000000000000000..1f5b82cf74c5f045ef427eea434181d8d33d0f78
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diff --git a/extract/embeddings/stability/tfn_pretrained/meta.json b/extract/embeddings/stability/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3b979192cba14330b38154e68b892f081168c7f6
--- /dev/null
+++ b/extract/embeddings/stability/tfn_pretrained/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "tfn_pretrained",
+ "family": "registry",
+ "target": "tfn_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/tfn_pretrained/best.pt",
+ "checkpoint_sha256": "17af58de61a4674c",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 39 of 39 tensors",
+ "weights_sha256": "a7afc00e258bf380",
+ "n_parameters": 250880,
+ "task": "stability",
+ "date": "2026-09-19 20:17",
+ "seconds": 22.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
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+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
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+  "nan_values": 0,
+  "all_zero_rows": 0,
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+  "numerical_rank": 109,
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+  "verdict": "pass"
+ }
+}