diff --git a/confirmation_downstream/embeddings/ec_classification/ankh_base/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/ankh_base/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/ec_classification/ankh_base/meta.json b/confirmation_downstream/embeddings/ec_classification/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..19c485f6a5eb983860f256c4344acf363f3cffaf
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 17:00",
+ "seconds": 59.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1674,
+  "numerical_rank": 768,
+  "max_abs": 0.7743563652038574
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/ec_classification/esm2_650m/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm2_650m/ids_test.txt
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diff --git a/confirmation_downstream/embeddings/ec_classification/esm2_650m/meta.json b/confirmation_downstream/embeddings/ec_classification/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5fcfc1bbe70647f1cc51a2c13cf4cf04543f6899
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 16:59",
+ "seconds": 87.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1674,
+  "numerical_rank": 1279,
+  "max_abs": 8.526667594909668
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/ec_classification/esm3/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm3/ids_test.txt
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diff --git a/confirmation_downstream/embeddings/ec_classification/esm3/meta.json b/confirmation_downstream/embeddings/ec_classification/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0024ab87ef10c3d206e476ff5bb0288ce715033d
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 17:05",
+ "seconds": 267.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1536,
+  "max_abs": 9253.294921875
+ },
+ "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/confirmation_downstream/embeddings/ec_classification/esm_if1/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm_if1/ids_test.txt
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diff --git a/confirmation_downstream/embeddings/ec_classification/esm_if1/meta.json b/confirmation_downstream/embeddings/ec_classification/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..89cfaf6f8f6d6f50d3303b482d2d764a35dcd35d
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 17:07",
+ "seconds": 157.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 511,
+  "max_abs": 0.9411705732345581
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038824098366321,
+  "rel_change_coord_swap": 0.4455433661584478,
+  "rel_change_seq_shuffle": 3.609444983503181e-07,
+  "rel_change_rigid_motion": 1.1007018105063154e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/ec_classification/proteinmpnn/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/proteinmpnn/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/ec_classification/proteinmpnn/meta.json b/confirmation_downstream/embeddings/ec_classification/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3c22bdb8eea5127d314232135759a7a748abfc97
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 17:08",
+ "seconds": 14.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1999,
+  "numerical_rank": 127,
+  "max_abs": 2.458974838256836
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/ids_test.txt b/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e015e9bdba6f31a0206148bc6778fa43946b3a37
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..11e6d53bff63480d99309f184e59da2762371026
--- /dev/null
+++ b/confirmation_downstream/embeddings/ec_classification/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ec_classification",
+ "date": "2026-09-22 17:19",
+ "seconds": 73.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ec_classification.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_ec_classification.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1677,
+  "numerical_rank": 1024,
+  "max_abs": 0.3229963481426239
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/ankh_base/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/ankh_base/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/ankh_base/meta.json b/confirmation_downstream/embeddings/fluorescence/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6ffec13b469d90cd91d107a602051fd7e41409f3
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 16:59",
+ "seconds": 59.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 768,
+  "max_abs": 0.36801794171333313
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/esm1b/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm1b/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/esm1b/meta.json b/confirmation_downstream/embeddings/fluorescence/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..92e817737d22d7112cd4fa45ad72c4b7b2ebce61
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm1b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:41",
+ "seconds": 22.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 15.597543716430664
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/esm2_3b/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm2_3b/ids_test.txt
@@ -0,0 +1,2000 @@
+gfp__test_000014
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diff --git a/confirmation_downstream/embeddings/fluorescence/esm2_3b/meta.json b/confirmation_downstream/embeddings/fluorescence/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..16fbd8e26d18631a7263f49c0201037677b20805
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm2_3b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:41",
+ "seconds": 29.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1999,
+  "max_abs": 14.228243827819824
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/esm2_650m/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm2_650m/ids_test.txt
@@ -0,0 +1,2000 @@
+gfp__test_000014
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diff --git a/confirmation_downstream/embeddings/fluorescence/esm2_650m/meta.json b/confirmation_downstream/embeddings/fluorescence/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..fd984cc9c0f6dc6797b6a88e35b1834c235d34fa
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 17:19",
+ "seconds": 61.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 8.505927085876465
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/esm3/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm3/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/esm3/meta.json b/confirmation_downstream/embeddings/fluorescence/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..10c4d4999c5467d8f2d72e9186da00cebe489924
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 17:03",
+ "seconds": 220.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1536,
+  "max_abs": 9026.7001953125
+ },
+ "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/confirmation_downstream/embeddings/fluorescence/esm_if1/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm_if1/ids_test.txt
@@ -0,0 +1,2000 @@
+gfp__test_000014
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diff --git a/confirmation_downstream/embeddings/fluorescence/esm_if1/meta.json b/confirmation_downstream/embeddings/fluorescence/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..73e8e0dd6bc3f2cfc16786cf0da6fc4392c9aacf
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 17:05",
+ "seconds": 149.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 511,
+  "max_abs": 0.9045584201812744
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038824098366321,
+  "rel_change_coord_swap": 0.44554341448284107,
+  "rel_change_seq_shuffle": 3.6075331281840625e-07,
+  "rel_change_rigid_motion": 1.1023897986673931e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/foldseek_3di/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/foldseek_3di/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/foldseek_3di/meta.json b/confirmation_downstream/embeddings/fluorescence/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3aeeba38995880405729f2fba7e64f343f2fa603
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/foldseek_3di/meta.json
@@ -0,0 +1,38 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:44",
+ "seconds": 2.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 19,
+  "max_abs": 0.37552741169929504
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/meta.json b/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6a712887fd3c3c9c83fd4488ee037758db91003b
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/gearnet_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet_pretrained",
+ "family": "registry",
+ "target": "gearnet_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/gearnet/mc_gearnet_edge.pth",
+ "checkpoint_sha256": "6dc11e2db6eff3c9",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "9eaaa8a2c8a79a37",
+ "n_parameters": 20145635,
+ "task": "fluorescence",
+ "date": "2026-09-22 19:44",
+ "seconds": 113.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 512,
+  "max_abs": 11.043222427368164
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126984702319132,
+  "rel_change_coord_swap": 0.8348703850808867,
+  "rel_change_seq_shuffle": 0.9662573225933023,
+  "rel_change_rigid_motion": 1.3047187541504715e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/meta.json b/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ced6ad5ce984a4a6ab0e08f92114a72a35f282b4
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/ipa_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa_pretrained",
+ "family": "registry",
+ "target": "ipa_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "checkpoint": "checkpoints/ipa_pretrained/best.pt",
+ "checkpoint_sha256": "cd4ca8e7f61daba2",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 95 of 95 tensors",
+ "weights_sha256": "d858a2f47e2041f3",
+ "n_parameters": 648016,
+ "task": "fluorescence",
+ "date": "2026-09-22 19:45",
+ "seconds": 5.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 128,
+  "max_abs": 0.7180326581001282
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.3578874371238928,
+  "rel_change_coord_swap": 0.35089059818670276,
+  "rel_change_seq_shuffle": 0.229386638791794,
+  "rel_change_rigid_motion": 4.390786617610691e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/meta.json b/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..8d2ae7ef2a14805a9170788e7f4b70c9ae4e249c
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:45",
+ "seconds": 8.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 3.1943576335906982
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/prostt5/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/prostt5/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/prostt5/meta.json b/confirmation_downstream/embeddings/fluorescence/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..339f377e1197c1177fe09ccb06ac159e4c1fe770
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/prostt5/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:42",
+ "seconds": 20.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 0.6092288494110107
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/protbert_bfd/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/protbert_bfd/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/protbert_bfd/meta.json b/confirmation_downstream/embeddings/fluorescence/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cfe24eaa3b0a87b399febced654d91934b05987c
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/protbert_bfd/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:42",
+ "seconds": 12.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1023,
+  "max_abs": 1.5259732007980347
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/proteinmpnn/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/proteinmpnn/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/proteinmpnn/meta.json b/confirmation_downstream/embeddings/fluorescence/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7ed8dab722118f74a1704eae104f2330ed187926
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 17:06",
+ "seconds": 19.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 2.24159574508667
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/saprot/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
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diff --git a/confirmation_downstream/embeddings/fluorescence/saprot/meta.json b/confirmation_downstream/embeddings/fluorescence/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..56f10a5cbbf1c337d9fe8c13dc8850db2fd98241
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/saprot/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:42",
+ "seconds": 46.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 1.0033109188079834
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bcffd989e4903191ffb3312cff9d865b367b919f
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/meta.json b/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5e7fa097cc9be45df224c8583763ae57150c7d61
--- /dev/null
+++ b/confirmation_downstream/embeddings/fluorescence/tfn_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "fluorescence",
+ "date": "2026-09-22 19:45",
+ "seconds": 5.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/fluorescence.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_fluorescence.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 112,
+  "max_abs": 0.7046182751655579
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03822254801769116,
+  "rel_change_coord_swap": 0.07263558999286251,
+  "rel_change_seq_shuffle": 0.28095587451507054,
+  "rel_change_rigid_motion": 9.573661210872962e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_bp/ankh_base/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
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diff --git a/confirmation_downstream/embeddings/go_bp/ankh_base/meta.json b/confirmation_downstream/embeddings/go_bp/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1ed294d3b355f0af6116fefd3361b80a953f51e8
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "go_bp",
+ "date": "2026-09-22 17:20",
+ "seconds": 17.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 768,
+  "max_abs": 0.7396242618560791
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_bp/esm2_650m/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/esm2_650m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm2_650m/ids_valid.txt
@@ -0,0 +1,907 @@
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diff --git a/confirmation_downstream/embeddings/go_bp/esm2_650m/meta.json b/confirmation_downstream/embeddings/go_bp/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ead46162f24d5b3c6e0ce8f637cc453e1fd977e5
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "go_bp",
+ "date": "2026-09-22 16:58",
+ "seconds": 35.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 906,
+  "max_abs": 8.539515495300293
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_bp/esm3/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/esm3/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm3/ids_valid.txt
@@ -0,0 +1,907 @@
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diff --git a/confirmation_downstream/embeddings/go_bp/esm3/meta.json b/confirmation_downstream/embeddings/go_bp/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d4bbfef045aa1dd00ee67d91af0c3d2db0256d69
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "go_bp",
+ "date": "2026-09-22 17:21",
+ "seconds": 69.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 906,
+  "max_abs": 9039.6796875
+ },
+ "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/confirmation_downstream/embeddings/go_bp/esm_if1/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/esm_if1/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm_if1/ids_valid.txt
@@ -0,0 +1,907 @@
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diff --git a/confirmation_downstream/embeddings/go_bp/esm_if1/meta.json b/confirmation_downstream/embeddings/go_bp/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..04e76a8a96e6c6f60e866c22f01ccc609160eafe
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "go_bp",
+ "date": "2026-09-22 17:01",
+ "seconds": 152.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 511,
+  "max_abs": 1.101523756980896
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822055183396,
+  "rel_change_coord_swap": 0.44554345045628896,
+  "rel_change_seq_shuffle": 3.76796040101069e-07,
+  "rel_change_rigid_motion": 1.1093354809109465e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_bp/proteinmpnn/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/proteinmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/proteinmpnn/ids_valid.txt
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diff --git a/confirmation_downstream/embeddings/go_bp/proteinmpnn/meta.json b/confirmation_downstream/embeddings/go_bp/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ca415edcba5561e6ca1af3eb3f7a5d2afd2dd821
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "go_bp",
+ "date": "2026-09-22 17:01",
+ "seconds": 11.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 127,
+  "max_abs": 2.24920654296875
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/ids_valid.txt b/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bde0a6401e8489e586ef4568dd4b759f0f4a2c5b
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/ids_valid.txt
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diff --git a/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d17cf86a75b3334404542e5d2f4f3c0cfa75d8b9
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_bp/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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_bp",
+ "date": "2026-09-22 17:19",
+ "seconds": 17.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_bp.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_bp.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 907
+ },
+ "health": {
+  "n_rows": 907,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 907,
+  "numerical_rank": 906,
+  "max_abs": 0.3982395529747009
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_mf/ankh_base/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/ankh_base/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/ankh_base/meta.json b/confirmation_downstream/embeddings/go_mf/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..97e47630c8bce3a0bb6b4d21a8b2c8162d973424
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "go_mf",
+ "date": "2026-09-22 17:09",
+ "seconds": 30.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 768,
+  "max_abs": 0.7149300575256348
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_mf/esm2_650m/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/esm2_650m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm2_650m/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/esm2_650m/meta.json b/confirmation_downstream/embeddings/go_mf/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e4d47f6e8fe98fc01af580fa3719ea59689589a4
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "go_mf",
+ "date": "2026-09-22 17:08",
+ "seconds": 22.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 1032,
+  "max_abs": 8.529074668884277
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_mf/esm3/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/esm3/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm3/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/esm3/meta.json b/confirmation_downstream/embeddings/go_mf/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f0eaaca2be634c4a99d208fdaaa0c431d8a54ac3
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "go_mf",
+ "date": "2026-09-22 17:11",
+ "seconds": 114.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 1032,
+  "max_abs": 9194.4287109375
+ },
+ "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/confirmation_downstream/embeddings/go_mf/esm_if1/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/esm_if1/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm_if1/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/esm_if1/meta.json b/confirmation_downstream/embeddings/go_mf/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0b33e3c1397e2258263cb2744d5d12c9a0e5b9eb
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "go_mf",
+ "date": "2026-09-22 17:12",
+ "seconds": 45.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 511,
+  "max_abs": 1.143680453300476
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822048167173,
+  "rel_change_coord_swap": 0.4455433849587538,
+  "rel_change_seq_shuffle": 3.7089917072828197e-07,
+  "rel_change_rigid_motion": 1.1095585718306348e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_mf/proteinmpnn/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/proteinmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/proteinmpnn/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/proteinmpnn/meta.json b/confirmation_downstream/embeddings/go_mf/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f84808affb21252fca94738e28becbbfa20a55f8
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "go_mf",
+ "date": "2026-09-22 17:12",
+ "seconds": 7.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 127,
+  "max_abs": 2.2603795528411865
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt b/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb2e1f945ba0d542f4028f3c7b0bb42feec3e94e
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/ids_valid.txt
@@ -0,0 +1,1033 @@
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diff --git a/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2688daa24c5d3b2fa4cd494ebc3ce89cd3458515
--- /dev/null
+++ b/confirmation_downstream/embeddings/go_mf/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 17:09",
+ "seconds": 34.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/go_mf.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_go_mf.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 1033
+ },
+ "health": {
+  "n_rows": 1033,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1033,
+  "numerical_rank": 1024,
+  "max_abs": 0.3951055407524109
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/ankh_base/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/ankh_base/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/ankh_base/meta.json b/confirmation_downstream/embeddings/membrane_soluble/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..23438da9d15751060c66fe134d7c6c8a3f4173b0
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 17:01",
+ "seconds": 75.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 768,
+  "max_abs": 0.6937401294708252
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm1b/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm1b/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm1b/meta.json b/confirmation_downstream/embeddings/membrane_soluble/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0c999a7a59aa55bef7fa83553cbd39daddbf7af1
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm1b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:28",
+ "seconds": 35.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1279,
+  "max_abs": 17.807741165161133
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/meta.json b/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..050d90222a70e9debef7085474eb93aeda729f98
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm2_3b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:28",
+ "seconds": 51.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1691,
+  "max_abs": 14.486713409423828
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/meta.json b/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..11a8bcd89f923a88ff9fd11663363796fa71ea5c
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 16:58",
+ "seconds": 47.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1279,
+  "max_abs": 8.511129379272461
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm3/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm3/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm3/meta.json b/confirmation_downstream/embeddings/membrane_soluble/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4683fe52447052294e4acfbbc3e29f76182329f6
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 17:05",
+ "seconds": 266.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1536,
+  "max_abs": 8724.48046875
+ },
+ "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/confirmation_downstream/embeddings/membrane_soluble/esm_if1/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm_if1/ids_test.txt
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/esm_if1/meta.json b/confirmation_downstream/embeddings/membrane_soluble/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..d0f0f3826ce14975ec0a1bf8445f66ab8b13b0dc
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 17:07",
+ "seconds": 144.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 511,
+  "max_abs": 1.2780234813690186
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822996000798,
+  "rel_change_coord_swap": 0.445543383018016,
+  "rel_change_seq_shuffle": 3.698398388073932e-07,
+  "rel_change_rigid_motion": 1.1060181134713752e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/meta.json b/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..87844682ea359aa0858bad2d0d0fdcdb84a847e6
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/foldseek_3di/meta.json
@@ -0,0 +1,38 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:32",
+ "seconds": 5.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1691,
+  "numerical_rank": 19,
+  "max_abs": 0.9894366264343262
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/meta.json b/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..44f23871f306d7044b2e0513fb7efe4ed78494be
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/gearnet_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet_pretrained",
+ "family": "registry",
+ "target": "gearnet_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/gearnet/mc_gearnet_edge.pth",
+ "checkpoint_sha256": "6dc11e2db6eff3c9",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "9eaaa8a2c8a79a37",
+ "n_parameters": 20145635,
+ "task": "membrane_soluble",
+ "date": "2026-09-22 19:32",
+ "seconds": 156.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 512,
+  "max_abs": 157.8610076904297
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126984881141899,
+  "rel_change_coord_swap": 0.8348703678855703,
+  "rel_change_seq_shuffle": 0.9662573634491042,
+  "rel_change_rigid_motion": 1.1957254400632916e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/meta.json b/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..76e190a85c38f13d41b12a31302840111d2630a5
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/ipa_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa_pretrained",
+ "family": "registry",
+ "target": "ipa_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "checkpoint": "checkpoints/ipa_pretrained/best.pt",
+ "checkpoint_sha256": "cd4ca8e7f61daba2",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 95 of 95 tensors",
+ "weights_sha256": "d858a2f47e2041f3",
+ "n_parameters": 648016,
+ "task": "membrane_soluble",
+ "date": "2026-09-22 19:33",
+ "seconds": 5.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 128,
+  "max_abs": 0.961031973361969
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.35788758264242265,
+  "rel_change_coord_swap": 0.3508904172664656,
+  "rel_change_seq_shuffle": 0.22938646599604673,
+  "rel_change_rigid_motion": 4.359663094916371e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/meta.json b/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e900bcb3bb4827b8cfcc8956739a4c0c84ea6c69
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:32",
+ "seconds": 8.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 127,
+  "max_abs": 3.303626537322998
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/prostt5/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/prostt5/ids_test.txt
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/prostt5/meta.json b/confirmation_downstream/embeddings/membrane_soluble/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6c46d01d836bf265a49d32d5322f6a72e5dd27f0
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/prostt5/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:29",
+ "seconds": 34.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1024,
+  "max_abs": 1.1670100688934326
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/meta.json b/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..33e9c19fc73edb915654023bb49be3039a78afc5
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/protbert_bfd/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:29",
+ "seconds": 18.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1023,
+  "max_abs": 1.9610179662704468
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/meta.json b/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..50323bf4210367d84a742b7d4695d2ddbcdb0aca
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 17:08",
+ "seconds": 10.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 127,
+  "max_abs": 2.247851848602295
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2e770f20b8d18185ce487056ae2cdeb409c5fbc2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 16:59",
+ "seconds": 93.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1024,
+  "max_abs": 0.5117433071136475
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/saprot/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/saprot/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/saprot/meta.json b/confirmation_downstream/embeddings/membrane_soluble/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c8bd84ee0a52ca7fd2d6cc253de086aa2e415048
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/saprot/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:15",
+ "seconds": 106.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 1279,
+  "max_abs": 1.5615063905715942
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d54054c3db4968dfe5164f13e01a1604873b4b2
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt
@@ -0,0 +1,1692 @@
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diff --git a/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/meta.json b/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ecda24e365a0cbe32a45cd6ddbd6fc3f61f5cfb7
--- /dev/null
+++ b/confirmation_downstream/embeddings/membrane_soluble/tfn_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "membrane_soluble",
+ "date": "2026-09-22 19:32",
+ "seconds": 4.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_membrane_soluble.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 1692
+ },
+ "health": {
+  "n_rows": 1692,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1692,
+  "numerical_rank": 107,
+  "max_abs": 1.2006168365478516
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03822254761126085,
+  "rel_change_coord_swap": 0.07263558411946638,
+  "rel_change_seq_shuffle": 0.2809558820749094,
+  "rel_change_rigid_motion": 9.408354918862136e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/remote_homology/ankh_base/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/ankh_base/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/ankh_base/ids_train.txt
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diff --git a/confirmation_downstream/embeddings/remote_homology/ankh_base/meta.json b/confirmation_downstream/embeddings/remote_homology/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7415523c2794fb394302ae7cfd7641d8b1d8c261
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:03",
+ "seconds": 36.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 768,
+  "max_abs": 0.920002281665802
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/remote_homology/esm2_650m/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/esm2_650m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm2_650m/ids_train.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/remote_homology/esm2_650m/meta.json b/confirmation_downstream/embeddings/remote_homology/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..759ae65bef90f60074df0d55236e43d872297d26
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:19",
+ "seconds": 51.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 8.974336624145508
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/remote_homology/esm3/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/esm3/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm3/ids_train.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/remote_homology/esm3/meta.json b/confirmation_downstream/embeddings/remote_homology/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..55e2cd167ebb5f64f93cf2107aed7831bafa1cc8
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:21",
+ "seconds": 107.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1536,
+  "max_abs": 9211.2099609375
+ },
+ "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/confirmation_downstream/embeddings/remote_homology/esm_if1/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/esm_if1/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm_if1/ids_train.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/remote_homology/esm_if1/meta.json b/confirmation_downstream/embeddings/remote_homology/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..bb645dfe55627dce2c77661c93fe21d0938e7524
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:05",
+ "seconds": 148.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 511,
+  "max_abs": 1.0816513299942017
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822793102065,
+  "rel_change_coord_swap": 0.44554343102883365,
+  "rel_change_seq_shuffle": 3.9070047011772544e-07,
+  "rel_change_rigid_motion": 1.1075199244267232e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/remote_homology/proteinmpnn/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/proteinmpnn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/proteinmpnn/ids_train.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/remote_homology/proteinmpnn/meta.json b/confirmation_downstream/embeddings/remote_homology/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..faf3a85f26ed654cc27ab434135f1aec300fb797
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:06",
+ "seconds": 20.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 2.531156539916992
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt b/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44b8dc516f10a2ce1c158be71f3b113eb9927a79
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0471440978c0423d5596164024d2cc9ac42eb4bd
--- /dev/null
+++ b/confirmation_downstream/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "remote_homology",
+ "date": "2026-09-22 17:19",
+ "seconds": 27.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_remote_homology.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "train": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 0.3615911304950714
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/ankh_base/ids_test.txt b/confirmation_downstream/embeddings/stability/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/ankh_base/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
+EEHEE_rd3_0037.pdb_A20K__test_000025
+EEHEE_rd3_0037.pdb_A20Q__test_000030
+EEHEE_rd3_0037.pdb_A20S__test_000032
+EEHEE_rd3_0037.pdb_A22K__test_000043
+EEHEE_rd3_0037.pdb_A22M__test_000045
+EEHEE_rd3_0037.pdb_A22P__test_000047
+EEHEE_rd3_0037.pdb_A22T__test_000051
+EEHEE_rd3_0037.pdb_A22V__test_000052
+EEHEE_rd3_0037.pdb_A23F__test_000057
+EEHEE_rd3_0037.pdb_A23L__test_000062
+EEHEE_rd3_0037.pdb_A23Q__test_000066
+EEHEE_rd3_0037.pdb_D29A__test_000073
+EEHEE_rd3_0037.pdb_D29G__test_000076
+EEHEE_rd3_0037.pdb_D29N__test_000082
+EEHEE_rd3_0037.pdb_D29V__test_000088
+EEHEE_rd3_0037.pdb_E17V__test_000106
+EEHEE_rd3_0037.pdb_E31F__test_000111
+EEHEE_rd3_0037.pdb_E31S__test_000122
+EEHEE_rd3_0037.pdb_E9D__test_000128
+EEHEE_rd3_0037.pdb_E9F__test_000129
+EEHEE_rd3_0037.pdb_E9M__test_000135
+EEHEE_rd3_0037.pdb_G36T__test_000159
+EEHEE_rd3_0037.pdb_G7H__test_000167
+EEHEE_rd3_0037.pdb_G7R__test_000175
+EEHEE_rd3_0037.pdb_G7V__test_000178
+EEHEE_rd3_0037.pdb_H35L__test_000188
+EEHEE_rd3_0037.pdb_H35V__test_000196
+EEHEE_rd3_0037.pdb_I34D__test_000200
+EEHEE_rd3_0037.pdb_I34F__test_000202
+EEHEE_rd3_0037.pdb_I34Q__test_000210
+EEHEE_rd3_0037.pdb_I3F__test_000220
+EEHEE_rd3_0037.pdb_I3G__test_000221
+EEHEE_rd3_0037.pdb_I3N__test_000226
+EEHEE_rd3_0037.pdb_I3Y__test_000234
+EEHEE_rd3_0037.pdb_K21A__test_000235
+EEHEE_rd3_0037.pdb_K21L__test_000242
+EEHEE_rd3_0037.pdb_K21M__test_000243
+EEHEE_rd3_0037.pdb_K21Y__test_000252
+EEHEE_rd3_0037.pdb_K24F__test_000256
+EEHEE_rd3_0037.pdb_K24M__test_000261
+EEHEE_rd3_0037.pdb_K24T__test_000267
+EEHEE_rd3_0037.pdb_K25E__test_000273
+EEHEE_rd3_0037.pdb_K25I__test_000277
+EEHEE_rd3_0037.pdb_K25L__test_000278
+EEHEE_rd3_0037.pdb_K25M__test_000279
+EEHEE_rd3_0037.pdb_K40W__test_000305
+EEHEE_rd3_0037.pdb_K4S__test_000320
+EEHEE_rd3_0037.pdb_K4T__test_000321
+EEHEE_rd3_0037.pdb_K4V__test_000322
+EEHEE_rd3_0037.pdb_L14D__test_000326
+EEHEE_rd3_0037.pdb_L14E__test_000327
+EEHEE_rd3_0037.pdb_L14F__test_000328
+EEHEE_rd3_0037.pdb_N6I__test_000367
+EEHEE_rd3_0037.pdb_N6T__test_000375
+EEHEE_rd3_0037.pdb_N6W__test_000377
+EEHEE_rd3_0037.pdb_P13R__test_000391
+EEHEE_rd3_0037.pdb_P16D__test_000398
+EEHEE_rd3_0037.pdb_P16I__test_000403
+EEHEE_rd3_0037.pdb_P16T__test_000411
+EEHEE_rd3_0037.pdb_P16W__test_000413
+EEHEE_rd3_0037.pdb_P28D__test_000416
+EEHEE_rd3_0037.pdb_P28L__test_000423
+EEHEE_rd3_0037.pdb_P28Y__test_000432
+EEHEE_rd3_0037.pdb_Q18A__test_000433
+EEHEE_rd3_0037.pdb_Q18D__test_000434
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+villin_G33H__test_012441
+villin_G33N__test_012446
+villin_G33T__test_012451
+villin_K24A__test_012455
+villin_K24I__test_012461
+villin_K24V__test_012470
+villin_K29A__test_012473
+villin_K29I__test_012479
+villin_K29L__test_012480
+villin_K29M__test_012481
+villin_K30A__test_012491
+villin_K30H__test_012496
+villin_K30M__test_012499
+villin_K30V__test_012506
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+villin_K7N__test_012536
+villin_K7P__test_012537
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+villin_L20M__test_012571
+villin_L20V__test_012578
+villin_L22G__test_012585
+villin_L22K__test_012588
+villin_L22P__test_012591
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+villin_L22T__test_012595
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+villin_L28F__test_012602
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+villin_L34E__test_012619
+villin_L34M__test_012625
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+villin_L34T__test_012631
+villin_L34W__test_012633
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+villin_M12A__test_012635
+villin_M12E__test_012637
+villin_M12F__test_012638
+villin_M12R__test_012647
+villin_N19E__test_012655
+villin_N19G__test_012657
+villin_N27H__test_012676
+villin_P21L__test_012697
+villin_P21Q__test_012700
+villin_P21S__test_012702
+villin_P21W__test_012705
+villin_Q25L__test_012715
+villin_Q26A__test_012725
+villin_Q26E__test_012727
+villin_R14A__test_012743
+villin_R14E__test_012745
+villin_R14F__test_012746
+villin_R14H__test_012748
+villin_R14K__test_012750
+villin_R14M__test_012752
+villin_R14P__test_012754
+villin_R14S__test_012756
+villin_R14V__test_012758
+villin_S15E__test_012763
+villin_S15K__test_012768
+villin_S15R__test_012774
+villin_S15V__test_012776
+villin_T13Q__test_012809
+villin_T13R__test_012810
+villin_V9M__test_012824
+villin_V9N__test_012825
+villin_W23E__test_012835
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diff --git a/confirmation_downstream/embeddings/stability/ankh_base/meta.json b/confirmation_downstream/embeddings/stability/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ffd78cc35b14716cd4d88bfc0aa01787fc0b8994
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "stability",
+ "date": "2026-09-22 17:06",
+ "seconds": 11.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 767,
+  "max_abs": 0.7521985769271851
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/esm1b/ids_test.txt b/confirmation_downstream/embeddings/stability/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm1b/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
+EEHEE_rd3_0037.pdb_A20K__test_000025
+EEHEE_rd3_0037.pdb_A20Q__test_000030
+EEHEE_rd3_0037.pdb_A20S__test_000032
+EEHEE_rd3_0037.pdb_A22K__test_000043
+EEHEE_rd3_0037.pdb_A22M__test_000045
+EEHEE_rd3_0037.pdb_A22P__test_000047
+EEHEE_rd3_0037.pdb_A22T__test_000051
+EEHEE_rd3_0037.pdb_A22V__test_000052
+EEHEE_rd3_0037.pdb_A23F__test_000057
+EEHEE_rd3_0037.pdb_A23L__test_000062
+EEHEE_rd3_0037.pdb_A23Q__test_000066
+EEHEE_rd3_0037.pdb_D29A__test_000073
+EEHEE_rd3_0037.pdb_D29G__test_000076
+EEHEE_rd3_0037.pdb_D29N__test_000082
+EEHEE_rd3_0037.pdb_D29V__test_000088
+EEHEE_rd3_0037.pdb_E17V__test_000106
+EEHEE_rd3_0037.pdb_E31F__test_000111
+EEHEE_rd3_0037.pdb_E31S__test_000122
+EEHEE_rd3_0037.pdb_E9D__test_000128
+EEHEE_rd3_0037.pdb_E9F__test_000129
+EEHEE_rd3_0037.pdb_E9M__test_000135
+EEHEE_rd3_0037.pdb_G36T__test_000159
+EEHEE_rd3_0037.pdb_G7H__test_000167
+EEHEE_rd3_0037.pdb_G7R__test_000175
+EEHEE_rd3_0037.pdb_G7V__test_000178
+EEHEE_rd3_0037.pdb_H35L__test_000188
+EEHEE_rd3_0037.pdb_H35V__test_000196
+EEHEE_rd3_0037.pdb_I34D__test_000200
+EEHEE_rd3_0037.pdb_I34F__test_000202
+EEHEE_rd3_0037.pdb_I34Q__test_000210
+EEHEE_rd3_0037.pdb_I3F__test_000220
+EEHEE_rd3_0037.pdb_I3G__test_000221
+EEHEE_rd3_0037.pdb_I3N__test_000226
+EEHEE_rd3_0037.pdb_I3Y__test_000234
+EEHEE_rd3_0037.pdb_K21A__test_000235
+EEHEE_rd3_0037.pdb_K21L__test_000242
+EEHEE_rd3_0037.pdb_K21M__test_000243
+EEHEE_rd3_0037.pdb_K21Y__test_000252
+EEHEE_rd3_0037.pdb_K24F__test_000256
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+EEHEE_rd3_0037.pdb_K25M__test_000279
+EEHEE_rd3_0037.pdb_K40W__test_000305
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+EEHEE_rd3_0037.pdb_K4V__test_000322
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+EEHEE_rd3_0037.pdb_L14E__test_000327
+EEHEE_rd3_0037.pdb_L14F__test_000328
+EEHEE_rd3_0037.pdb_N6I__test_000367
+EEHEE_rd3_0037.pdb_N6T__test_000375
+EEHEE_rd3_0037.pdb_N6W__test_000377
+EEHEE_rd3_0037.pdb_P13R__test_000391
+EEHEE_rd3_0037.pdb_P16D__test_000398
+EEHEE_rd3_0037.pdb_P16I__test_000403
+EEHEE_rd3_0037.pdb_P16T__test_000411
+EEHEE_rd3_0037.pdb_P16W__test_000413
+EEHEE_rd3_0037.pdb_P28D__test_000416
+EEHEE_rd3_0037.pdb_P28L__test_000423
+EEHEE_rd3_0037.pdb_P28Y__test_000432
+EEHEE_rd3_0037.pdb_Q18A__test_000433
+EEHEE_rd3_0037.pdb_Q18D__test_000434
+EEHEE_rd3_0037.pdb_Q18G__test_000437
+EEHEE_rd3_0037.pdb_Q18R__test_000445
+EEHEE_rd3_0037.pdb_Q33I__test_000457
+EEHEE_rd3_0037.pdb_Q33M__test_000460
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+EEHEE_rd3_0037.pdb_R43H__test_000510
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+EEHEE_rd3_0037.pdb_R43W__test_000521
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+EEHEE_rd3_0037.pdb_S15Q__test_000535
+EEHEE_rd3_0037.pdb_S15Y__test_000540
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+EEHEE_rd3_0037.pdb_T1Q__test_000571
+EEHEE_rd3_0037.pdb_T2I__test_000583
+EEHEE_rd3_0037.pdb_T2L__test_000585
+EEHEE_rd3_0037.pdb_T2P__test_000588
+EEHEE_rd3_0037.pdb_T2R__test_000590
+EEHEE_rd3_0037.pdb_T2W__test_000593
+EEHEE_rd3_0037.pdb_T38E__test_000597
+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
+EEHEE_rd3_0037.pdb_V12M__test_000640
+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
+EEHEE_rd3_0037.pdb_V5F__test_000706
+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
+EEHEE_rd3_0037.pdb_W27T__test_000736
+EEHEE_rd3_0037.pdb_Y10E__test_000741
+EEHEE_rd3_0037.pdb_Y10M__test_000748
+EEHEE_rd3_0037.pdb_Y10P__test_000750
+EEHEE_rd3_0037.pdb_Y30E__test_000759
+EEHEE_rd3_0037.pdb_Y30P__test_000768
+EEHEE_rd3_1498.pdb_A18H__test_000780
+EEHEE_rd3_1498.pdb_A21E__test_000795
+EEHEE_rd3_1498.pdb_A21H__test_000798
+EEHEE_rd3_1498.pdb_A21T__test_000808
+EEHEE_rd3_1498.pdb_A22N__test_000821
+EEHEE_rd3_1498.pdb_A26G__test_000833
+EEHEE_rd3_1498.pdb_A26V__test_000845
+EEHEE_rd3_1498.pdb_E16G__test_000851
+EEHEE_rd3_1498.pdb_E16H__test_000852
+EEHEE_rd3_1498.pdb_E16K__test_000854
+EEHEE_rd3_1498.pdb_E16N__test_000857
+EEHEE_rd3_1498.pdb_E32A__test_000866
+EEHEE_rd3_1498.pdb_E32L__test_000873
+EEHEE_rd3_1498.pdb_E32N__test_000875
+EEHEE_rd3_1498.pdb_E32R__test_000878
+EEHEE_rd3_1498.pdb_F25D__test_000885
+EEHEE_rd3_1498.pdb_F25N__test_000893
+EEHEE_rd3_1498.pdb_F25P__test_000894
+EEHEE_rd3_1498.pdb_F25S__test_000897
+EEHEE_rd3_1498.pdb_G1D__test_000903
+EEHEE_rd3_1498.pdb_G1T__test_000916
+EEHEE_rd3_1498.pdb_G1W__test_000918
+EEHEE_rd3_1498.pdb_G37D__test_000921
+EEHEE_rd3_1498.pdb_G37F__test_000923
+EEHEE_rd3_1498.pdb_G37Q__test_000931
+EEHEE_rd3_1498.pdb_G7D__test_000939
+EEHEE_rd3_1498.pdb_G7Q__test_000949
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+EEHEE_rd3_1498.pdb_H36F__test_000959
+EEHEE_rd3_1498.pdb_H36V__test_000971
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+EEHEE_rd3_1498.pdb_H41F__test_000977
+EEHEE_rd3_1498.pdb_H41W__test_000990
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+EEHEE_rd3_1498.pdb_H43R__test_001004
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+EEHEE_rd3_1498.pdb_H4S__test_001023
+EEHEE_rd3_1498.pdb_I19Q__test_001039
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+EEHEE_rd3_1498.pdb_K11I__test_001052
+EEHEE_rd3_1498.pdb_K17A__test_001064
+EEHEE_rd3_1498.pdb_K17E__test_001066
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+EEHEE_rd3_1702.pdb_G6Y__test_001694
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diff --git a/confirmation_downstream/embeddings/stability/esm1b/meta.json b/confirmation_downstream/embeddings/stability/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..743c430daa482e81f978723a56f61d3c593063e5
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm1b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 19:45",
+ "seconds": 8.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 17.898534774780273
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/esm2_3b/ids_test.txt b/confirmation_downstream/embeddings/stability/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm2_3b/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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+EEHEE_rd3_0037.pdb_A20E__test_000020
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+EEHEE_rd3_0037.pdb_T1Q__test_000571
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+EEHEE_rd3_0037.pdb_T2R__test_000590
+EEHEE_rd3_0037.pdb_T2W__test_000593
+EEHEE_rd3_0037.pdb_T38E__test_000597
+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
+EEHEE_rd3_0037.pdb_V12M__test_000640
+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
+EEHEE_rd3_0037.pdb_V5F__test_000706
+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
+EEHEE_rd3_0037.pdb_W27T__test_000736
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+villin_V9N__test_012825
+villin_W23E__test_012835
+villin_W23G__test_012837
+villin_W23H__test_012838
+villin_W23M__test_012842
+villin_W23R__test_012846
diff --git a/confirmation_downstream/embeddings/stability/esm2_3b/meta.json b/confirmation_downstream/embeddings/stability/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f81fa5d91f99cd914552b7dc3b09731c60177f46
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm2_3b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 19:45",
+ "seconds": 9.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1999,
+  "max_abs": 14.219295501708984
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/esm2_650m/ids_test.txt b/confirmation_downstream/embeddings/stability/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm2_650m/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
+EEHEE_rd3_0037.pdb_A20K__test_000025
+EEHEE_rd3_0037.pdb_A20Q__test_000030
+EEHEE_rd3_0037.pdb_A20S__test_000032
+EEHEE_rd3_0037.pdb_A22K__test_000043
+EEHEE_rd3_0037.pdb_A22M__test_000045
+EEHEE_rd3_0037.pdb_A22P__test_000047
+EEHEE_rd3_0037.pdb_A22T__test_000051
+EEHEE_rd3_0037.pdb_A22V__test_000052
+EEHEE_rd3_0037.pdb_A23F__test_000057
+EEHEE_rd3_0037.pdb_A23L__test_000062
+EEHEE_rd3_0037.pdb_A23Q__test_000066
+EEHEE_rd3_0037.pdb_D29A__test_000073
+EEHEE_rd3_0037.pdb_D29G__test_000076
+EEHEE_rd3_0037.pdb_D29N__test_000082
+EEHEE_rd3_0037.pdb_D29V__test_000088
+EEHEE_rd3_0037.pdb_E17V__test_000106
+EEHEE_rd3_0037.pdb_E31F__test_000111
+EEHEE_rd3_0037.pdb_E31S__test_000122
+EEHEE_rd3_0037.pdb_E9D__test_000128
+EEHEE_rd3_0037.pdb_E9F__test_000129
+EEHEE_rd3_0037.pdb_E9M__test_000135
+EEHEE_rd3_0037.pdb_G36T__test_000159
+EEHEE_rd3_0037.pdb_G7H__test_000167
+EEHEE_rd3_0037.pdb_G7R__test_000175
+EEHEE_rd3_0037.pdb_G7V__test_000178
+EEHEE_rd3_0037.pdb_H35L__test_000188
+EEHEE_rd3_0037.pdb_H35V__test_000196
+EEHEE_rd3_0037.pdb_I34D__test_000200
+EEHEE_rd3_0037.pdb_I34F__test_000202
+EEHEE_rd3_0037.pdb_I34Q__test_000210
+EEHEE_rd3_0037.pdb_I3F__test_000220
+EEHEE_rd3_0037.pdb_I3G__test_000221
+EEHEE_rd3_0037.pdb_I3N__test_000226
+EEHEE_rd3_0037.pdb_I3Y__test_000234
+EEHEE_rd3_0037.pdb_K21A__test_000235
+EEHEE_rd3_0037.pdb_K21L__test_000242
+EEHEE_rd3_0037.pdb_K21M__test_000243
+EEHEE_rd3_0037.pdb_K21Y__test_000252
+EEHEE_rd3_0037.pdb_K24F__test_000256
+EEHEE_rd3_0037.pdb_K24M__test_000261
+EEHEE_rd3_0037.pdb_K24T__test_000267
+EEHEE_rd3_0037.pdb_K25E__test_000273
+EEHEE_rd3_0037.pdb_K25I__test_000277
+EEHEE_rd3_0037.pdb_K25L__test_000278
+EEHEE_rd3_0037.pdb_K25M__test_000279
+EEHEE_rd3_0037.pdb_K40W__test_000305
+EEHEE_rd3_0037.pdb_K4S__test_000320
+EEHEE_rd3_0037.pdb_K4T__test_000321
+EEHEE_rd3_0037.pdb_K4V__test_000322
+EEHEE_rd3_0037.pdb_L14D__test_000326
+EEHEE_rd3_0037.pdb_L14E__test_000327
+EEHEE_rd3_0037.pdb_L14F__test_000328
+EEHEE_rd3_0037.pdb_N6I__test_000367
+EEHEE_rd3_0037.pdb_N6T__test_000375
+EEHEE_rd3_0037.pdb_N6W__test_000377
+EEHEE_rd3_0037.pdb_P13R__test_000391
+EEHEE_rd3_0037.pdb_P16D__test_000398
+EEHEE_rd3_0037.pdb_P16I__test_000403
+EEHEE_rd3_0037.pdb_P16T__test_000411
+EEHEE_rd3_0037.pdb_P16W__test_000413
+EEHEE_rd3_0037.pdb_P28D__test_000416
+EEHEE_rd3_0037.pdb_P28L__test_000423
+EEHEE_rd3_0037.pdb_P28Y__test_000432
+EEHEE_rd3_0037.pdb_Q18A__test_000433
+EEHEE_rd3_0037.pdb_Q18D__test_000434
+EEHEE_rd3_0037.pdb_Q18G__test_000437
+EEHEE_rd3_0037.pdb_Q18R__test_000445
+EEHEE_rd3_0037.pdb_Q33I__test_000457
+EEHEE_rd3_0037.pdb_Q33M__test_000460
+EEHEE_rd3_0037.pdb_Q8K__test_000476
+EEHEE_rd3_0037.pdb_Q8L__test_000477
+EEHEE_rd3_0037.pdb_Q8P__test_000480
+EEHEE_rd3_0037.pdb_R26A__test_000487
+EEHEE_rd3_0037.pdb_R26F__test_000490
+EEHEE_rd3_0037.pdb_R43A__test_000505
+EEHEE_rd3_0037.pdb_R43E__test_000507
+EEHEE_rd3_0037.pdb_R43G__test_000509
+EEHEE_rd3_0037.pdb_R43H__test_000510
+EEHEE_rd3_0037.pdb_R43I__test_000511
+EEHEE_rd3_0037.pdb_R43K__test_000512
+EEHEE_rd3_0037.pdb_R43T__test_000519
+EEHEE_rd3_0037.pdb_R43W__test_000521
+EEHEE_rd3_0037.pdb_S15E__test_000525
+EEHEE_rd3_0037.pdb_S15G__test_000527
+EEHEE_rd3_0037.pdb_S15Q__test_000535
+EEHEE_rd3_0037.pdb_S15Y__test_000540
+EEHEE_rd3_0037.pdb_T11S__test_000555
+EEHEE_rd3_0037.pdb_T1K__test_000566
+EEHEE_rd3_0037.pdb_T1Q__test_000571
+EEHEE_rd3_0037.pdb_T2I__test_000583
+EEHEE_rd3_0037.pdb_T2L__test_000585
+EEHEE_rd3_0037.pdb_T2P__test_000588
+EEHEE_rd3_0037.pdb_T2R__test_000590
+EEHEE_rd3_0037.pdb_T2W__test_000593
+EEHEE_rd3_0037.pdb_T38E__test_000597
+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
+EEHEE_rd3_0037.pdb_V12M__test_000640
+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
+EEHEE_rd3_0037.pdb_V5F__test_000706
+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
+EEHEE_rd3_0037.pdb_W27T__test_000736
+EEHEE_rd3_0037.pdb_Y10E__test_000741
+EEHEE_rd3_0037.pdb_Y10M__test_000748
+EEHEE_rd3_0037.pdb_Y10P__test_000750
+EEHEE_rd3_0037.pdb_Y30E__test_000759
+EEHEE_rd3_0037.pdb_Y30P__test_000768
+EEHEE_rd3_1498.pdb_A18H__test_000780
+EEHEE_rd3_1498.pdb_A21E__test_000795
+EEHEE_rd3_1498.pdb_A21H__test_000798
+EEHEE_rd3_1498.pdb_A21T__test_000808
+EEHEE_rd3_1498.pdb_A22N__test_000821
+EEHEE_rd3_1498.pdb_A26G__test_000833
+EEHEE_rd3_1498.pdb_A26V__test_000845
+EEHEE_rd3_1498.pdb_E16G__test_000851
+EEHEE_rd3_1498.pdb_E16H__test_000852
+EEHEE_rd3_1498.pdb_E16K__test_000854
+EEHEE_rd3_1498.pdb_E16N__test_000857
+EEHEE_rd3_1498.pdb_E32A__test_000866
+EEHEE_rd3_1498.pdb_E32L__test_000873
+EEHEE_rd3_1498.pdb_E32N__test_000875
+EEHEE_rd3_1498.pdb_E32R__test_000878
+EEHEE_rd3_1498.pdb_F25D__test_000885
+EEHEE_rd3_1498.pdb_F25N__test_000893
+EEHEE_rd3_1498.pdb_F25P__test_000894
+EEHEE_rd3_1498.pdb_F25S__test_000897
+EEHEE_rd3_1498.pdb_G1D__test_000903
+EEHEE_rd3_1498.pdb_G1T__test_000916
+EEHEE_rd3_1498.pdb_G1W__test_000918
+EEHEE_rd3_1498.pdb_G37D__test_000921
+EEHEE_rd3_1498.pdb_G37F__test_000923
+EEHEE_rd3_1498.pdb_G37Q__test_000931
+EEHEE_rd3_1498.pdb_G7D__test_000939
+EEHEE_rd3_1498.pdb_G7Q__test_000949
+EEHEE_rd3_1498.pdb_H36E__test_000958
+EEHEE_rd3_1498.pdb_H36F__test_000959
+EEHEE_rd3_1498.pdb_H36V__test_000971
+EEHEE_rd3_1498.pdb_H41E__test_000976
+EEHEE_rd3_1498.pdb_H41F__test_000977
+EEHEE_rd3_1498.pdb_H41W__test_000990
+EEHEE_rd3_1498.pdb_H43D__test_000993
+EEHEE_rd3_1498.pdb_H43G__test_000996
+EEHEE_rd3_1498.pdb_H43R__test_001004
+EEHEE_rd3_1498.pdb_H4N__test_001019
+EEHEE_rd3_1498.pdb_H4S__test_001023
+EEHEE_rd3_1498.pdb_I19Q__test_001039
+EEHEE_rd3_1498.pdb_I19W__test_001044
+EEHEE_rd3_1498.pdb_K11I__test_001052
+EEHEE_rd3_1498.pdb_K17A__test_001064
+EEHEE_rd3_1498.pdb_K17E__test_001066
+EEHEE_rd3_1498.pdb_K17G__test_001068
+EEHEE_rd3_1498.pdb_K17H__test_001069
+EEHEE_rd3_1498.pdb_K17P__test_001074
+EEHEE_rd3_1498.pdb_K17W__test_001080
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+EEHEE_rd3_1498.pdb_K20N__test_001091
+EEHEE_rd3_1498.pdb_K20S__test_001095
+EEHEE_rd3_1498.pdb_K20W__test_001098
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+EEHEE_rd3_1498.pdb_K24F__test_001121
+EEHEE_rd3_1498.pdb_K24G__test_001122
+EEHEE_rd3_1498.pdb_K24H__test_001123
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+EEHEE_rd3_1498.pdb_K27T__test_001150
+EEHEE_rd3_1498.pdb_K28F__test_001157
+EEHEE_rd3_1498.pdb_K28G__test_001158
+EEHEE_rd3_1498.pdb_L15D__test_001173
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+EEHEE_rd3_1498.pdb_L31E__test_001192
+EEHEE_rd3_1498.pdb_L31S__test_001203
+EEHEE_rd3_1498.pdb_L3A__test_001208
+EEHEE_rd3_1498.pdb_L3H__test_001213
+EEHEE_rd3_1498.pdb_L3K__test_001215
+EEHEE_rd3_1498.pdb_L3N__test_001217
+EEHEE_rd3_1498.pdb_L3W__test_001224
+EEHEE_rd3_1498.pdb_L5A__test_001226
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+EEHEE_rd3_1498.pdb_L5Y__test_001243
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+EEHEE_rd3_1498.pdb_P13D__test_001299
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+EEHEE_rd3_1702.pdb_G6Y__test_001694
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+EEHEE_rd3_1702.pdb_I40G__test_001771
+EEHEE_rd3_1702.pdb_I40L__test_001774
+EEHEE_rd3_1702.pdb_K11H__test_001790
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+EEHEE_rd3_1702.pdb_K11Y__test_001802
+EEHEE_rd3_1702.pdb_K16D__test_001804
+EEHEE_rd3_1702.pdb_K16G__test_001807
+EEHEE_rd3_1702.pdb_K17H__test_001826
+EEHEE_rd3_1702.pdb_K17N__test_001830
+EEHEE_rd3_1702.pdb_K23F__test_001842
+EEHEE_rd3_1702.pdb_K23H__test_001844
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+EEHEE_rd3_1702.pdb_K36N__test_001920
+EEHEE_rd3_1702.pdb_K36V__test_001926
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diff --git a/confirmation_downstream/embeddings/stability/esm2_650m/meta.json b/confirmation_downstream/embeddings/stability/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cdfed4ab237966f00603fb03123c0ed3ed7e88d2
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 17:06",
+ "seconds": 13.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 8.510926246643066
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/esm3/ids_test.txt b/confirmation_downstream/embeddings/stability/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm3/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
+EEHEE_rd3_0037.pdb_V12M__test_000640
+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
+EEHEE_rd3_0037.pdb_V5F__test_000706
+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
+EEHEE_rd3_0037.pdb_W27T__test_000736
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+EEHEE_rd3_0037.pdb_Y30P__test_000768
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+EEHEE_rd3_1498.pdb_A21E__test_000795
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+EEHEE_rd3_1498.pdb_A21T__test_000808
+EEHEE_rd3_1498.pdb_A22N__test_000821
+EEHEE_rd3_1498.pdb_A26G__test_000833
+EEHEE_rd3_1498.pdb_A26V__test_000845
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+EEHEE_rd3_1498.pdb_E32A__test_000866
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+EEHEE_rd3_1498.pdb_F25S__test_000897
+EEHEE_rd3_1498.pdb_G1D__test_000903
+EEHEE_rd3_1498.pdb_G1T__test_000916
+EEHEE_rd3_1498.pdb_G1W__test_000918
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+EEHEE_rd3_1498.pdb_G7D__test_000939
+EEHEE_rd3_1498.pdb_G7Q__test_000949
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+EEHEE_rd3_1498.pdb_H36V__test_000971
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+EEHEE_rd3_1498.pdb_H41F__test_000977
+EEHEE_rd3_1498.pdb_H41W__test_000990
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+EEHEE_rd3_1498.pdb_H43G__test_000996
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diff --git a/confirmation_downstream/embeddings/stability/esm3/meta.json b/confirmation_downstream/embeddings/stability/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..44d84fb8002708c88fa3e7e651ad6266497850e7
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "2026-09-22 17:08",
+ "seconds": 92.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1536,
+  "max_abs": 8622.1396484375
+ },
+ "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/confirmation_downstream/embeddings/stability/esm_if1/ids_test.txt b/confirmation_downstream/embeddings/stability/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm_if1/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
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diff --git a/confirmation_downstream/embeddings/stability/esm_if1/meta.json b/confirmation_downstream/embeddings/stability/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a45355fc25dd89af853b94902aeb97a26e0990ee
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "2026-09-22 17:11",
+ "seconds": 165.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 511,
+  "max_abs": 0.9354055523872375
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822793102065,
+  "rel_change_coord_swap": 0.4455434152778429,
+  "rel_change_seq_shuffle": 3.6548032638888556e-07,
+  "rel_change_rigid_motion": 1.1063516530467213e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/foldseek_3di/ids_test.txt b/confirmation_downstream/embeddings/stability/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/foldseek_3di/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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+EEHEE_rd3_0037.pdb_T42G__test_000617
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+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
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+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
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+EEHEE_rd3_1498.pdb_A22N__test_000821
+EEHEE_rd3_1498.pdb_A26G__test_000833
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+EEHEE_rd3_1498.pdb_G1T__test_000916
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diff --git a/confirmation_downstream/embeddings/stability/foldseek_3di/meta.json b/confirmation_downstream/embeddings/stability/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ae6ef9c5e66edd94e1cc486dabed9621249fb399
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/foldseek_3di/meta.json
@@ -0,0 +1,38 @@
+{
+ "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": "2026-09-22 19:47",
+ "seconds": 1.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 932,
+  "numerical_rank": 19,
+  "max_abs": 0.7209302186965942
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/gearnet_pretrained/ids_test.txt b/confirmation_downstream/embeddings/stability/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/gearnet_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
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diff --git a/confirmation_downstream/embeddings/stability/gearnet_pretrained/meta.json b/confirmation_downstream/embeddings/stability/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c93a48623373507de20a8ed0e99118d90471735d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/gearnet_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet_pretrained",
+ "family": "registry",
+ "target": "gearnet_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/gearnet/mc_gearnet_edge.pth",
+ "checkpoint_sha256": "6dc11e2db6eff3c9",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "9eaaa8a2c8a79a37",
+ "n_parameters": 20145635,
+ "task": "stability",
+ "date": "2026-09-22 19:47",
+ "seconds": 35.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 512,
+  "max_abs": 61.69620895385742
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126985501292669,
+  "rel_change_coord_swap": 0.8348703340556809,
+  "rel_change_seq_shuffle": 0.9662573090118363,
+  "rel_change_rigid_motion": 1.1802141137767095e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/ipa_pretrained/ids_test.txt b/confirmation_downstream/embeddings/stability/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/ipa_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
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+EEHEE_rd3_0037.pdb_A20Q__test_000030
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+EEHEE_rd3_0037.pdb_A22K__test_000043
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+EEHEE_rd3_0037.pdb_A22V__test_000052
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+EEHEE_rd3_0037.pdb_A23L__test_000062
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+EEHEE_rd3_0037.pdb_E9D__test_000128
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+EEHEE_rd3_0037.pdb_I34Q__test_000210
+EEHEE_rd3_0037.pdb_I3F__test_000220
+EEHEE_rd3_0037.pdb_I3G__test_000221
+EEHEE_rd3_0037.pdb_I3N__test_000226
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+EEHEE_rd3_0037.pdb_P13R__test_000391
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+EEHEE_rd3_0037.pdb_P28D__test_000416
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+EEHEE_rd3_0037.pdb_Q18A__test_000433
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+EEHEE_rd3_0037.pdb_T2W__test_000593
+EEHEE_rd3_0037.pdb_T38E__test_000597
+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
+EEHEE_rd3_0037.pdb_V12M__test_000640
+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
+EEHEE_rd3_0037.pdb_V5F__test_000706
+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
+EEHEE_rd3_0037.pdb_W27T__test_000736
+EEHEE_rd3_0037.pdb_Y10E__test_000741
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+EEHEE_rd3_0037.pdb_Y10P__test_000750
+EEHEE_rd3_0037.pdb_Y30E__test_000759
+EEHEE_rd3_0037.pdb_Y30P__test_000768
+EEHEE_rd3_1498.pdb_A18H__test_000780
+EEHEE_rd3_1498.pdb_A21E__test_000795
+EEHEE_rd3_1498.pdb_A21H__test_000798
+EEHEE_rd3_1498.pdb_A21T__test_000808
+EEHEE_rd3_1498.pdb_A22N__test_000821
+EEHEE_rd3_1498.pdb_A26G__test_000833
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+EEHEE_rd3_1498.pdb_E16H__test_000852
+EEHEE_rd3_1498.pdb_E16K__test_000854
+EEHEE_rd3_1498.pdb_E16N__test_000857
+EEHEE_rd3_1498.pdb_E32A__test_000866
+EEHEE_rd3_1498.pdb_E32L__test_000873
+EEHEE_rd3_1498.pdb_E32N__test_000875
+EEHEE_rd3_1498.pdb_E32R__test_000878
+EEHEE_rd3_1498.pdb_F25D__test_000885
+EEHEE_rd3_1498.pdb_F25N__test_000893
+EEHEE_rd3_1498.pdb_F25P__test_000894
+EEHEE_rd3_1498.pdb_F25S__test_000897
+EEHEE_rd3_1498.pdb_G1D__test_000903
+EEHEE_rd3_1498.pdb_G1T__test_000916
+EEHEE_rd3_1498.pdb_G1W__test_000918
+EEHEE_rd3_1498.pdb_G37D__test_000921
+EEHEE_rd3_1498.pdb_G37F__test_000923
+EEHEE_rd3_1498.pdb_G37Q__test_000931
+EEHEE_rd3_1498.pdb_G7D__test_000939
+EEHEE_rd3_1498.pdb_G7Q__test_000949
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+EEHEE_rd3_1498.pdb_H36V__test_000971
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+EEHEE_rd3_1498.pdb_K17E__test_001066
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diff --git a/confirmation_downstream/embeddings/stability/ipa_pretrained/meta.json b/confirmation_downstream/embeddings/stability/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9136c9abaee4f66fa2fe7448581a366f0ba98356
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/ipa_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa_pretrained",
+ "family": "registry",
+ "target": "ipa_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "checkpoint": "checkpoints/ipa_pretrained/best.pt",
+ "checkpoint_sha256": "cd4ca8e7f61daba2",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 95 of 95 tensors",
+ "weights_sha256": "d858a2f47e2041f3",
+ "n_parameters": 648016,
+ "task": "stability",
+ "date": "2026-09-22 19:47",
+ "seconds": 5.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 128,
+  "max_abs": 0.9736275672912598
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.3578876078720534,
+  "rel_change_coord_swap": 0.35089036704039184,
+  "rel_change_seq_shuffle": 0.22938661227984752,
+  "rel_change_rigid_motion": 4.409816448036471e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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+villin_M12R__test_012647
+villin_N19E__test_012655
+villin_N19G__test_012657
+villin_N27H__test_012676
+villin_P21L__test_012697
+villin_P21Q__test_012700
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+villin_P21W__test_012705
+villin_Q25L__test_012715
+villin_Q26A__test_012725
+villin_Q26E__test_012727
+villin_R14A__test_012743
+villin_R14E__test_012745
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+villin_R14V__test_012758
+villin_S15E__test_012763
+villin_S15K__test_012768
+villin_S15R__test_012774
+villin_S15V__test_012776
+villin_T13Q__test_012809
+villin_T13R__test_012810
+villin_V9M__test_012824
+villin_V9N__test_012825
+villin_W23E__test_012835
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+villin_W23H__test_012838
+villin_W23M__test_012842
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diff --git a/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/meta.json b/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..17e595d4603dda544beac8b0aba8f527b9a76c41
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "2026-09-22 19:47",
+ "seconds": 6.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 3.287599802017212
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/prostt5/ids_test.txt b/confirmation_downstream/embeddings/stability/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/prostt5/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
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+EEHEE_rd3_0037.pdb_V41E__test_000687
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+EEHEE_rd3_0037.pdb_V5L__test_000711
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diff --git a/confirmation_downstream/embeddings/stability/prostt5/meta.json b/confirmation_downstream/embeddings/stability/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..19fcda202f63794ea36f6206ff612ea256681a2e
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/prostt5/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 19:46",
+ "seconds": 7.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 0.8907023668289185
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/protbert_bfd/ids_test.txt b/confirmation_downstream/embeddings/stability/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/protbert_bfd/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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+EEHEE_rd3_0037.pdb_T42D__test_000614
+EEHEE_rd3_0037.pdb_T42G__test_000617
+EEHEE_rd3_0037.pdb_T42P__test_000624
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+EEHEE_rd3_0037.pdb_V12N__test_000641
+EEHEE_rd3_0037.pdb_V12P__test_000642
+EEHEE_rd3_0037.pdb_V32F__test_000652
+EEHEE_rd3_0037.pdb_V32S__test_000663
+EEHEE_rd3_0037.pdb_V39H__test_000672
+EEHEE_rd3_0037.pdb_V41E__test_000687
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+EEHEE_rd3_0037.pdb_V5L__test_000711
+EEHEE_rd3_0037.pdb_W27E__test_000723
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+EEHEE_rd3_1498.pdb_A22N__test_000821
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+EEHEE_rd3_1498.pdb_E32A__test_000866
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+EEHEE_rd3_1498.pdb_G1D__test_000903
+EEHEE_rd3_1498.pdb_G1T__test_000916
+EEHEE_rd3_1498.pdb_G1W__test_000918
+EEHEE_rd3_1498.pdb_G37D__test_000921
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diff --git a/confirmation_downstream/embeddings/stability/protbert_bfd/meta.json b/confirmation_downstream/embeddings/stability/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f4e7184db7ea2de8b288e5b4779cc92722e27934
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/protbert_bfd/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 19:46",
+ "seconds": 5.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1023,
+  "max_abs": 1.4881961345672607
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/proteinmpnn/ids_test.txt b/confirmation_downstream/embeddings/stability/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/proteinmpnn/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
+EEHEE_rd3_0037.pdb_A20F__test_000021
+EEHEE_rd3_0037.pdb_A20K__test_000025
+EEHEE_rd3_0037.pdb_A20Q__test_000030
+EEHEE_rd3_0037.pdb_A20S__test_000032
+EEHEE_rd3_0037.pdb_A22K__test_000043
+EEHEE_rd3_0037.pdb_A22M__test_000045
+EEHEE_rd3_0037.pdb_A22P__test_000047
+EEHEE_rd3_0037.pdb_A22T__test_000051
+EEHEE_rd3_0037.pdb_A22V__test_000052
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+EEHEE_rd3_0037.pdb_A23L__test_000062
+EEHEE_rd3_0037.pdb_A23Q__test_000066
+EEHEE_rd3_0037.pdb_D29A__test_000073
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+EEHEE_rd3_0037.pdb_I3G__test_000221
+EEHEE_rd3_0037.pdb_I3N__test_000226
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diff --git a/confirmation_downstream/embeddings/stability/proteinmpnn/meta.json b/confirmation_downstream/embeddings/stability/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0ac4c3775ab404ccf213e0adb9a3b46dca733ac8
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "2026-09-22 17:11",
+ "seconds": 21.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 2.2165277004241943
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/ids_test.txt b/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/ids_test.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c38072035aa833a8432158634f4f045bf4a0fe77
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-22 17:06",
+ "seconds": 13.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 0.3464878797531128
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/saprot/ids_test.txt b/confirmation_downstream/embeddings/stability/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/saprot/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
+EEHEE_rd3_0037.pdb_A19R__test_000013
+EEHEE_rd3_0037.pdb_A20E__test_000020
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+EEHEE_rd3_0037.pdb_E17V__test_000106
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+EEHEE_rd3_0037.pdb_E31S__test_000122
+EEHEE_rd3_0037.pdb_E9D__test_000128
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+EEHEE_rd3_0037.pdb_E9M__test_000135
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diff --git a/confirmation_downstream/embeddings/stability/saprot/meta.json b/confirmation_downstream/embeddings/stability/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..66e35252a9d751b4c9e10fb0e7a3f5667bcdfc2a
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/saprot/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "2026-09-22 19:46",
+ "seconds": 25.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 1.1620049476623535
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/stability/tfn_pretrained/ids_test.txt b/confirmation_downstream/embeddings/stability/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50b584dfbb988d4d6038205b91aed76425bceb5d
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/tfn_pretrained/ids_test.txt
@@ -0,0 +1,2000 @@
+EEHEE_rd3_0037.pdb_A19L__test_000008
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diff --git a/confirmation_downstream/embeddings/stability/tfn_pretrained/meta.json b/confirmation_downstream/embeddings/stability/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..15cf71ddeb394911004da7ee9fd18fc1e6f74b4f
--- /dev/null
+++ b/confirmation_downstream/embeddings/stability/tfn_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "2026-09-22 19:47",
+ "seconds": 5.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/stability.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_stability.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 104,
+  "max_abs": 1.072878360748291
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03822253839690554,
+  "rel_change_coord_swap": 0.07263563193401132,
+  "rel_change_seq_shuffle": 0.2809558727288082,
+  "rel_change_rigid_motion": 9.753970680752956e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/ankh_base/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/ankh_base/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/ankh_base/meta.json b/confirmation_downstream/embeddings/subcellular_localization/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..913f9fbce0c45d8bf10807a3cf1b48a84313b50f
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:11",
+ "seconds": 52.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 768,
+  "max_abs": 0.6709309220314026
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm1b/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/esm1b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm1b/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm1b/meta.json b/confirmation_downstream/embeddings/subcellular_localization/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e0d3b3fb8b3f19dde3bc2c4d1d447176b3087d10
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm1b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:33",
+ "seconds": 41.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 17.826772689819336
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/meta.json b/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..8d8f4421e6fbf10842919c03d1d0e68941197b6d
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm2_3b/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:34",
+ "seconds": 59.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1999,
+  "max_abs": 14.548250198364258
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/meta.json b/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..1a7ceb8aed357a4723b6f959e298ff3f97bee6ad
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:09",
+ "seconds": 76.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 8.511129379272461
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm3/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/esm3/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm3/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm3/meta.json b/confirmation_downstream/embeddings/subcellular_localization/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5ac5538bd2ddab0ff351237b823ffcbf0888b6c5
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm3/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:14",
+ "seconds": 153.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1536,
+  "max_abs": 8735.759765625
+ },
+ "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/confirmation_downstream/embeddings/subcellular_localization/esm_if1/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/esm_if1/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm_if1/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/esm_if1/meta.json b/confirmation_downstream/embeddings/subcellular_localization/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..121f162401a1e7d6cbe40d82e675b89a79e0d763
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/esm_if1/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:15",
+ "seconds": 72.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 511,
+  "max_abs": 1.3104194402694702
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822793102065,
+  "rel_change_coord_swap": 0.44554339730969716,
+  "rel_change_seq_shuffle": 3.751704158890046e-07,
+  "rel_change_rigid_motion": 1.0983365618946212e-05,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/meta.json b/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ffe1b0c103a1737e59224ba64c0198d8f97971e4
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/foldseek_3di/meta.json
@@ -0,0 +1,38 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:40",
+ "seconds": 6.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 1999,
+  "numerical_rank": 19,
+  "max_abs": 0.9929577708244324
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/meta.json b/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2cecb741ec364b77d2256b4ef92bf6fcc6257000
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/gearnet_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet_pretrained",
+ "family": "registry",
+ "target": "gearnet_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/gearnet/mc_gearnet_edge.pth",
+ "checkpoint_sha256": "6dc11e2db6eff3c9",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "9eaaa8a2c8a79a37",
+ "n_parameters": 20145635,
+ "task": "subcellular_localization",
+ "date": "2026-09-22 19:40",
+ "seconds": 184.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 512,
+  "max_abs": 210.46133422851562
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126984392243746,
+  "rel_change_coord_swap": 0.8348703340556809,
+  "rel_change_seq_shuffle": 0.9662572713175315,
+  "rel_change_rigid_motion": 1.1655589839813548e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/meta.json b/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6af8e588ca0f3cf202cd3acf5942b77001b2e7a1
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/ipa_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa_pretrained",
+ "family": "registry",
+ "target": "ipa_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "checkpoint": "checkpoints/ipa_pretrained/best.pt",
+ "checkpoint_sha256": "cd4ca8e7f61daba2",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 95 of 95 tensors",
+ "weights_sha256": "d858a2f47e2041f3",
+ "n_parameters": 648016,
+ "task": "subcellular_localization",
+ "date": "2026-09-22 19:40",
+ "seconds": 5.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 128,
+  "max_abs": 1.0335502624511719
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.3578875363483409,
+  "rel_change_coord_swap": 0.35089050852116577,
+  "rel_change_seq_shuffle": 0.2293865025122066,
+  "rel_change_rigid_motion": 4.468027129227643e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json b/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..88dcd7b88d497a4878a066fb9baffed5e2e3eb3a
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,36 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:40",
+ "seconds": 9.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 3.303626537322998
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/prostt5/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/prostt5/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/prostt5/ids_valid.txt
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/prostt5/meta.json b/confirmation_downstream/embeddings/subcellular_localization/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..27051a4270176e4f12d389403b2f6d12e3f85dd0
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/prostt5/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:36",
+ "seconds": 39.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 1.1374393701553345
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/meta.json b/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4f0475a51a2e2db522c659bc8ae9ac2a81ab5f8b
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/protbert_bfd/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:36",
+ "seconds": 20.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1023,
+  "max_abs": 1.9610179662704468
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/meta.json b/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5a81f13b2019f759c1367d9faa63c97131bf99b9
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/proteinmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:15",
+ "seconds": 8.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 127,
+  "max_abs": 2.2507102489471436
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.2876636765789369,
+  "rel_change_coord_swap": 0.1046977269374211,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.6183316549153264e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/meta.json b/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9eb5c7eccdc2ab2f601819a12ab64be3da636f64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 17:10",
+ "seconds": 58.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1024,
+  "max_abs": 0.6131836175918579
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/saprot/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/saprot/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/saprot/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/saprot/meta.json b/confirmation_downstream/embeddings/subcellular_localization/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7b2f171cdf8f63dd5c2170669cb8b2250fd58d3a
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/saprot/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:35",
+ "seconds": 68.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 1279,
+  "max_abs": 2.203648805618286
+ },
+ "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"
+ }
+}
diff --git a/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt b/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e36569754933aecdda34309ccd3804714664e64
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt
@@ -0,0 +1,2000 @@
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diff --git a/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/meta.json b/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..351240fd0bca670e1750e4b731b70abdb9de45ae
--- /dev/null
+++ b/confirmation_downstream/embeddings/subcellular_localization/tfn_pretrained/meta.json
@@ -0,0 +1,39 @@
+{
+ "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": "subcellular_localization",
+ "date": "2026-09-22 19:40",
+ "seconds": 5.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "held-out cohort: protcompass/confirmation_downstream/ids_subcellular_localization.txt",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "valid": 2000
+ },
+ "health": {
+  "n_rows": 2000,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2000,
+  "numerical_rank": 107,
+  "max_abs": 1.8231700658798218
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03822255519960468,
+  "rel_change_coord_swap": 0.07263558049760618,
+  "rel_change_seq_shuffle": 0.28095589155091005,
+  "rel_change_rigid_motion": 9.9504562436845e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/probing_embeddings/esm2_3b/meta.json b/probing_embeddings/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..768e62106066a15970386c27b049c3b81121800b
--- /dev/null
+++ b/probing_embeddings/esm2_3b/meta.json
@@ -0,0 +1,21 @@
+{
+  "encoder": "esm2_3b",
+  "hub_id": "facebook/esm2_t36_3B_UR50D",
+  "revision": "476b639933c8baad5ad09a60ac1a87f987b656fc",
+  "layer": "final hidden state",
+  "special_tokens": "removed",
+  "dim": 2560,
+  "n_domains": 19461,
+  "n_residues": 2823525,
+  "dtype_compute": "torch.float16",
+  "dtype_stored": "float16",
+  "max_abs_value": 14.9609375,
+  "fp16_overflow": false,
+  "nonfinite_in_first_200k_rows": 0,
+  "distinct_pooled_rows": 19461,
+  "median_rel_change_under_sequence_shuffle": 0.39934101790216325,
+  "input": "sequence of the residues kept in labels.h5; discontinuous CATH domains are passed as one concatenated sequence",
+  "rows": "identical to residue/* rows of probing_data/labels.h5",
+  "seconds": 334.8,
+  "date": "2026-09-19"
+}
\ No newline at end of file
diff --git a/probing_embeddings/gvp/meta.json b/probing_embeddings/gvp/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9227b324d5269ddaa3059830229df65298fdb775
--- /dev/null
+++ b/probing_embeddings/gvp/meta.json
@@ -0,0 +1,35 @@
+{
+ "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",
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:37",
+ "seconds": 193.5,
+ "n_domains": 19461,
+ "dim": 116,
+ "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5",
+ "health": {
+  "n_rows": 19461,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 19461,
+  "numerical_rank": 115,
+  "max_abs": 2.8753087520599365
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03159192475562866,
+  "rel_change_coord_swap": 0.004911498440862752,
+  "rel_change_seq_shuffle": 0.0025094455675686604,
+  "rel_change_rigid_motion": 8.938065148643837e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/probing_embeddings/mace/meta.json b/probing_embeddings/mace/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..04405c38f29ec771f0aca955c92328b9bdffbe6a
--- /dev/null
+++ b/probing_embeddings/mace/meta.json
@@ -0,0 +1,33 @@
+{
+ "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,
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:31",
+ "seconds": 151.6,
+ "n_domains": 19461,
+ "dim": 128,
+ "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5",
+ "health": {
+  "n_rows": 19461,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 19461,
+  "numerical_rank": 127,
+  "max_abs": 1.098768949508667
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.015475071357416222,
+  "rel_change_coord_swap": 0.06619546880187852,
+  "rel_change_seq_shuffle": 0.04851771545213551,
+  "rel_change_rigid_motion": 1.4050815587066846e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/probing_embeddings/pottsmpnn_ft/meta.json b/probing_embeddings/pottsmpnn_ft/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ca2ecf45cfc5d8cdc6017ab1528331748c4fd808
--- /dev/null
+++ b/probing_embeddings/pottsmpnn_ft/meta.json
@@ -0,0 +1,32 @@
+{
+ "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,
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 19:54",
+ "seconds": 225.9,
+ "n_domains": 19461,
+ "dim": 128,
+ "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5",
+ "health": {
+  "n_rows": 19461,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 19461,
+  "numerical_rank": 127,
+  "max_abs": 2.603649139404297
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.681632164944024,
+  "rel_change_coord_swap": 0.1285565413937244,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 2.0394372754446537e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/probing_embeddings/prottrans_t5_xl_u50/meta.json b/probing_embeddings/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4537b87ad9f0b0ee8d15698acfbdd3a7ca80338d
--- /dev/null
+++ b/probing_embeddings/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,21 @@
+{
+  "encoder": "prottrans_t5_xl_u50",
+  "hub_id": "Rostlab/prot_t5_xl_half_uniref50-enc",
+  "revision": "94a6abc029ae13029317b140b7424e012bf8dfbf",
+  "layer": "final hidden state",
+  "special_tokens": "removed",
+  "dim": 1024,
+  "n_domains": 19461,
+  "n_residues": 2823525,
+  "dtype_compute": "torch.float16",
+  "dtype_stored": "float16",
+  "max_abs_value": 1.9501953125,
+  "fp16_overflow": false,
+  "nonfinite_in_first_200k_rows": 0,
+  "distinct_pooled_rows": 19461,
+  "median_rel_change_under_sequence_shuffle": 1.2735727018790566,
+  "input": "sequence of the residues kept in labels.h5; discontinuous CATH domains are passed as one concatenated sequence",
+  "rows": "identical to residue/* rows of probing_data/labels.h5",
+  "seconds": 126.2,
+  "date": "2026-09-19"
+}
\ No newline at end of file