diff --git a/extract/embeddings/remote_homology/esm2_3b/ids_test.txt b/extract/embeddings/remote_homology/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/esm2_3b/ids_test.txt
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diff --git a/extract/embeddings/remote_homology/esm2_3b/ids_train.txt b/extract/embeddings/remote_homology/esm2_3b/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/esm2_3b/ids_train.txt
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diff --git a/extract/embeddings/remote_homology/esm2_3b/ids_valid.txt b/extract/embeddings/remote_homology/esm2_3b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/esm2_3b/ids_valid.txt
@@ -0,0 +1,506 @@
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diff --git a/extract/embeddings/remote_homology/esm2_3b/meta.json b/extract/embeddings/remote_homology/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..26012a49bd8933bf2205ced2ccd3953b735d5332
--- /dev/null
+++ b/extract/embeddings/remote_homology/esm2_3b/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_3b",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t36_3B_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues; fp16 weights",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t36_3B_UR50D",
+ "checkpoint_revision": "476b639933c8baad5ad09a60ac1a87f987b656fc",
+ "dtype": "float16",
+ "hidden_size": 2560,
+ "n_layers": 36,
+ "n_parameters": 2835070881,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "remote_homology",
+ "date": "2026-09-20 11:15",
+ "seconds": 178.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6985,
+  "numerical_rank": 2559,
+  "max_abs": 14.5159912109375
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.16059037802733606,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/gcpnet_pretrained/ids_test.txt b/extract/embeddings/remote_homology/gcpnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/gcpnet_pretrained/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/gcpnet_pretrained/ids_valid.txt b/extract/embeddings/remote_homology/gcpnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/gcpnet_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/remote_homology/gcpnet_pretrained/meta.json b/extract/embeddings/remote_homology/gcpnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f7a31e951af6ab55d74692a495e62bb040d38c36
--- /dev/null
+++ b/extract/embeddings/remote_homology/gcpnet_pretrained/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "gcpnet_pretrained",
+ "family": "patched",
+ "target": "gcpnet_official",
+ "weights": "pretrained",
+ "rule": "official PSR model; 100 scalar channels + 16 vector norms, mean over the heavy atoms of each residue",
+ "env": "base",
+ "checkpoint": "external_repos/GCPNet/checkpoints/PSR/model_epoch_115_localpearson_0_616_localspearman_0_532_localkendall_0_385_globalpearson_0_871_globalspearman_0_869_globalkendall_0_676.ckpt",
+ "checkpoint_sha256": "ff7b73be01fb57d5",
+ "checkpoint_loaded_by": "strict=True",
+ "weights_sha256": "15bd126ac55f26a2",
+ "n_parameters": 1153181,
+ "inputs_passed": "all heavy atoms of the structure file (elements and coordinates); residue identity enters through side-chain atoms",
+ "patch": "patched/gcpnet_official.py",
+ "task": "remote_homology",
+ "date": "2026-09-20 11:28",
+ "seconds": 476.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 115,
+  "max_abs": 2.070418119430542
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.5457864701747894,
+  "rel_change_coord_swap": 0.26095230877399445,
+  "rel_change_seq_shuffle": 0.03569234535098076,
+  "rel_change_rigid_motion": 0.00025720152189023793,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/remote_homology/gvp/ids_test.txt b/extract/embeddings/remote_homology/gvp/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/gvp/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/gvp/ids_train.txt b/extract/embeddings/remote_homology/gvp/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/gvp/ids_train.txt
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diff --git a/extract/embeddings/remote_homology/gvp/ids_valid.txt b/extract/embeddings/remote_homology/gvp/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/gvp/ids_valid.txt
@@ -0,0 +1,506 @@
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diff --git a/extract/embeddings/remote_homology/gvp/meta.json b/extract/embeddings/remote_homology/gvp/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3e7e1d6d895c0633423ea851d8b9d6a2e95c8629
--- /dev/null
+++ b/extract/embeddings/remote_homology/gvp/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "gvp",
+ "family": "patched",
+ "target": "gvp_inproc",
+ "weights": "random",
+ "rule": "scalar channels + vector norms (invariant), masked mean",
+ "env": "base",
+ "weights_sha256": "4199962f00f771e2",
+ "seed": 20260919,
+ "n_parameters": 476935,
+ "inputs_passed": "backbone coordinates and residue identity",
+ "patch": "patched/gvp_inproc.py",
+ "task": "remote_homology",
+ "date": "2026-09-20 11:17",
+ "seconds": 28.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 115,
+  "max_abs": 2.8747382164001465
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03118545608185685,
+  "rel_change_coord_swap": 0.0063201406377201026,
+  "rel_change_seq_shuffle": 0.002777462957462268,
+  "rel_change_rigid_motion": 8.503984689595561e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/mace/ids_test.txt b/extract/embeddings/remote_homology/mace/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/mace/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/mace/ids_train.txt b/extract/embeddings/remote_homology/mace/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/mace/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/remote_homology/mace/ids_valid.txt b/extract/embeddings/remote_homology/mace/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/mace/ids_valid.txt
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diff --git a/extract/embeddings/remote_homology/mace/meta.json b/extract/embeddings/remote_homology/mace/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e61b6da73661d80324b1ef1533fffc08470ce529
--- /dev/null
+++ b/extract/embeddings/remote_homology/mace/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "mace",
+ "family": "registry",
+ "target": "mace",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "e8e9d6fd9722cc4e",
+ "n_parameters": 584064,
+ "task": "remote_homology",
+ "date": "2026-09-20 11:16",
+ "seconds": 23.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 127,
+  "max_abs": 1.2218812704086304
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.014915865242322838,
+  "rel_change_coord_swap": 0.05683945173750876,
+  "rel_change_seq_shuffle": 0.0523291422188011,
+  "rel_change_rigid_motion": 1.3602486243731065e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/pottsmpnn_ft/ids_test.txt b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_ft/ids_train.txt b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_train.txt
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_ft/ids_valid.txt b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_ft/ids_valid.txt
@@ -0,0 +1,506 @@
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_ft/meta.json b/extract/embeddings/remote_homology/pottsmpnn_ft/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a681c29110039b89d4ebafc3fc8f70118671211e
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_ft/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_ft",
+ "family": "registry",
+ "target": "pottsmpnn_ft_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "b8171c21b2e3eab7",
+ "n_parameters": 1712085,
+ "task": "remote_homology",
+ "date": "2026-09-20 11:19",
+ "seconds": 32.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 127,
+  "max_abs": 2.6449344158172607
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.5082692283690026,
+  "rel_change_coord_swap": 0.13421373340726975,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.330835728765909e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_test.txt b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_train.txt b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_valid.txt b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_soluble/ids_valid.txt
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diff --git a/extract/embeddings/remote_homology/pottsmpnn_soluble/meta.json b/extract/embeddings/remote_homology/pottsmpnn_soluble/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..801b834517476794c508c741a6615624c3c6e019
--- /dev/null
+++ b/extract/embeddings/remote_homology/pottsmpnn_soluble/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_soluble",
+ "family": "registry",
+ "target": "pottsmpnn_soluble_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "31f0aac7f4cefa1a",
+ "n_parameters": 1712085,
+ "task": "remote_homology",
+ "date": "2026-09-20 11:19",
+ "seconds": 34.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 127,
+  "max_abs": 2.085576057434082
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6675711994212048,
+  "rel_change_coord_swap": 0.17917227338286784,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.4140547445011483e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_test.txt b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_test.txt
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diff --git a/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_train.txt
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diff --git a/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_valid.txt b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/ids_valid.txt
@@ -0,0 +1,506 @@
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diff --git a/extract/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c7ac0633bc4fd61a0e76397021b513afcc1fe17c
--- /dev/null
+++ b/extract/embeddings/remote_homology/prottrans_t5_xl_u50/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "prottrans_t5_xl_u50",
+ "family": "hf_plm",
+ "target": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "Rostlab/prot_t5_xl_half_uniref50-enc",
+ "checkpoint_revision": "94a6abc029ae13029317b140b7424e012bf8dfbf",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208141824,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "remote_homology",
+ "date": "2026-09-20 11:12",
+ "seconds": 128.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6985,
+  "numerical_rank": 1024,
+  "max_abs": 0.4141782224178314
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.7503630666663541,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/remote_homology/saprot/ids_test.txt b/extract/embeddings/remote_homology/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4
--- /dev/null
+++ b/extract/embeddings/remote_homology/saprot/ids_test.txt
@@ -0,0 +1,480 @@
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diff --git a/extract/embeddings/remote_homology/saprot/ids_train.txt b/extract/embeddings/remote_homology/saprot/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4e0c924d77fe01396d2d467bba98ca569f08e71
--- /dev/null
+++ b/extract/embeddings/remote_homology/saprot/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/remote_homology/saprot/ids_valid.txt b/extract/embeddings/remote_homology/saprot/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f88db04867f54623be9ececc833379bbd563a8
--- /dev/null
+++ b/extract/embeddings/remote_homology/saprot/ids_valid.txt
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diff --git a/extract/embeddings/remote_homology/saprot/meta.json b/extract/embeddings/remote_homology/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..15c2670e59fb6adcd4197db7841a678950905c2b
--- /dev/null
+++ b/extract/embeddings/remote_homology/saprot/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "saprot",
+ "family": "patched",
+ "target": "saprot_hf",
+ "weights": "pretrained",
+ "rule": "final hidden states at the L residue positions of AA+3Di tokens",
+ "env": "base",
+ "checkpoint": "westlake-repl/SaProt_650M_AF2",
+ "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38",
+ "n_parameters": 651242901,
+ "inputs_passed": "amino-acid track: real sequence; 3Di track: real tokens from mini3di on the structure; no pLDDT masking",
+ "patch": "patched/saprot_hf.py",
+ "task": "remote_homology",
+ "date": "2026-09-20 11:30",
+ "seconds": 180.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/remote_homology.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 480,
+  "train": 6000,
+  "valid": 506
+ },
+ "health": {
+  "n_rows": 6986,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 6986,
+  "numerical_rank": 1279,
+  "max_abs": 1.3672527074813843
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.8705030813272382,
+  "rel_change_coord_swap": 0.4102216970171252,
+  "rel_change_seq_shuffle": 0.8413755808217256,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/ankh_base/ids_test.txt b/extract/embeddings/subcellular_localization/ankh_base/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ankh_base/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/ankh_base/ids_train.txt b/extract/embeddings/subcellular_localization/ankh_base/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ankh_base/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/ankh_base/ids_valid.txt b/extract/embeddings/subcellular_localization/ankh_base/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ankh_base/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/ankh_base/meta.json b/extract/embeddings/subcellular_localization/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9c717a2285722268185292cc275bb208ce88b11b
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ankh_base/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "ankh_base",
+ "family": "hf_plm",
+ "target": "ElnaggarLab/ankh-base",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "ElnaggarLab/ankh-base",
+ "checkpoint_revision": "d99cb6b966530dfc2ae96bc69d9255c2a07308b0",
+ "dtype": "float32",
+ "hidden_size": 768,
+ "n_layers": 48,
+ "n_parameters": 453170688,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:59",
+ "seconds": 325.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 768,
+  "max_abs": 0.6937402486801147
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.5002829140921271,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/cdconv/ids_test.txt b/extract/embeddings/subcellular_localization/cdconv/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/cdconv/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/cdconv/ids_train.txt b/extract/embeddings/subcellular_localization/cdconv/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/cdconv/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/subcellular_localization/cdconv/ids_valid.txt b/extract/embeddings/subcellular_localization/cdconv/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/cdconv/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/cdconv/meta.json b/extract/embeddings/subcellular_localization/cdconv/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..25b95dd4ee5e48b21f20bd2d04d1c06953f0e534
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/cdconv/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "cdconv",
+ "family": "registry",
+ "target": "cdconv",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "9203855665116c79",
+ "n_parameters": 619184,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:05",
+ "seconds": 76.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 256,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 256,
+  "max_abs": 0.20996303856372833
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.001572546549141407,
+  "rel_change_coord_swap": 0.011715235188603401,
+  "rel_change_seq_shuffle": 0.004441949771717191,
+  "rel_change_rigid_motion": 7.226870835097543e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/dimenet/ids_test.txt b/extract/embeddings/subcellular_localization/dimenet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/dimenet/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/dimenet/ids_train.txt b/extract/embeddings/subcellular_localization/dimenet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/dimenet/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/dimenet/ids_valid.txt b/extract/embeddings/subcellular_localization/dimenet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/dimenet/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/dimenet/meta.json b/extract/embeddings/subcellular_localization/dimenet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c524ab6c4e0ac6a1f6a4e64d5ac4971ab4ccfdcf
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/dimenet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "dimenet",
+ "family": "registry",
+ "target": "dimenet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "71e5f811f644cdf2",
+ "n_parameters": 362752,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:03",
+ "seconds": 23.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 1.3211644887924194
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.00359466125781171,
+  "rel_change_coord_swap": 0.005332541273893109,
+  "rel_change_seq_shuffle": 0.01124036381104809,
+  "rel_change_rigid_motion": 1.23831448402748e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm1b/ids_test.txt b/extract/embeddings/subcellular_localization/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm1b/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/esm1b/ids_train.txt b/extract/embeddings/subcellular_localization/esm1b/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm1b/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm1b/ids_valid.txt b/extract/embeddings/subcellular_localization/esm1b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm1b/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/esm1b/meta.json b/extract/embeddings/subcellular_localization/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0a88bdb7a055878eddb54ece788e057944db53a3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm1b/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm1b",
+ "family": "hf_plm",
+ "target": "facebook/esm1b_t33_650M_UR50S",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm1b_t33_650M_UR50S",
+ "checkpoint_revision": "7b37824baec4d3658e1df7479222a7c79b465b76",
+ "dtype": "float32",
+ "hidden_size": 1280,
+ "n_layers": 33,
+ "n_parameters": 650716821,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:45",
+ "seconds": 380.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1279,
+  "max_abs": 17.98320198059082
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.11968619571511047,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm2_150m/ids_test.txt b/extract/embeddings/subcellular_localization/esm2_150m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_150m/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_150m/ids_train.txt b/extract/embeddings/subcellular_localization/esm2_150m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_150m/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_150m/ids_valid.txt b/extract/embeddings/subcellular_localization/esm2_150m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_150m/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_150m/meta.json b/extract/embeddings/subcellular_localization/esm2_150m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..35f9d18defed73b02c5734dccc18e44a0c74c6dd
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_150m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_150m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t30_150M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t30_150M_UR50D",
+ "checkpoint_revision": "a695f6045e2e32885fa60af20c13cb35398ce30c",
+ "dtype": "float32",
+ "hidden_size": 640,
+ "n_layers": 30,
+ "n_parameters": 148385241,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:49",
+ "seconds": 159.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 640,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 639,
+  "max_abs": 7.333627223968506
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.23306057014528236,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm2_35m/ids_test.txt b/extract/embeddings/subcellular_localization/esm2_35m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_35m/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_35m/ids_train.txt b/extract/embeddings/subcellular_localization/esm2_35m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_35m/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_35m/ids_valid.txt b/extract/embeddings/subcellular_localization/esm2_35m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_35m/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_35m/meta.json b/extract/embeddings/subcellular_localization/esm2_35m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..413225b3166b1474fe7275046d36667ec6e4c9a1
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_35m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_35m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t12_35M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t12_35M_UR50D",
+ "checkpoint_revision": "6fbf070e65b0b7291e7bbcd451118c216cff79d8",
+ "dtype": "float32",
+ "hidden_size": 480,
+ "n_layers": 12,
+ "n_parameters": 33762001,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:46",
+ "seconds": 56.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 480,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 479,
+  "max_abs": 6.337296485900879
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.2002921266035882,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm2_3b/ids_test.txt b/extract/embeddings/subcellular_localization/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_3b/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_3b/ids_train.txt b/extract/embeddings/subcellular_localization/esm2_3b/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_3b/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_3b/ids_valid.txt b/extract/embeddings/subcellular_localization/esm2_3b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_3b/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_650m/ids_test.txt b/extract/embeddings/subcellular_localization/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_650m/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_650m/ids_train.txt b/extract/embeddings/subcellular_localization/esm2_650m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_650m/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_650m/ids_valid.txt b/extract/embeddings/subcellular_localization/esm2_650m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_650m/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_650m/meta.json b/extract/embeddings/subcellular_localization/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6734640c08f7af90cbe430788c4db8702944d5bb
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_650m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_650m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t33_650M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t33_650M_UR50D",
+ "checkpoint_revision": "08e4846e537177426273712802403f7ba8261b6c",
+ "dtype": "float32",
+ "hidden_size": 1280,
+ "n_layers": 33,
+ "n_parameters": 650714261,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:54",
+ "seconds": 402.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1279,
+  "max_abs": 8.65932846069336
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.18661678857220632,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm2_8m/ids_test.txt b/extract/embeddings/subcellular_localization/esm2_8m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_8m/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_8m/ids_train.txt b/extract/embeddings/subcellular_localization/esm2_8m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_8m/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/subcellular_localization/esm2_8m/ids_valid.txt b/extract/embeddings/subcellular_localization/esm2_8m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_8m/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/esm2_8m/meta.json b/extract/embeddings/subcellular_localization/esm2_8m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f1fed070ff4a92b672d0260080fc0709435a4e04
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm2_8m/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "esm2_8m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t6_8M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t6_8M_UR50D",
+ "checkpoint_revision": "c731040fcd8d73dceaa04b0a8e6329b345b0f5df",
+ "dtype": "float32",
+ "hidden_size": 320,
+ "n_layers": 6,
+ "n_parameters": 7737401,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:45",
+ "seconds": 25.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 320,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 319,
+  "max_abs": 5.301142692565918
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.2041863371369027,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/esm3/ids_test.txt b/extract/embeddings/subcellular_localization/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm3/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/esm3/ids_train.txt b/extract/embeddings/subcellular_localization/esm3/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm3/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm3/ids_valid.txt b/extract/embeddings/subcellular_localization/esm3/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm3/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/esm3/meta.json b/extract/embeddings/subcellular_localization/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..acf249b31b1620fc6cec13f3d319870ea24c7e90
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm3/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "esm3",
+ "family": "patched",
+ "target": "esm3_inproc",
+ "weights": "pretrained",
+ "rule": "final trunk residue embeddings, sequence and structure tracks",
+ "env": "base",
+ "checkpoint": "esm3-sm-open-v1/data/weights/esm3_sm_open_v1.pth",
+ "dtype": "bfloat16",
+ "n_parameters": 1401735748,
+ "inputs_passed": "sequence track: true residues; structure track: VQ-VAE tokens from the real backbone (N, CA, C, O, CB) plus coordinates for geometric attention; function, SASA and secondary-structure tracks at their defaults",
+ "patch": "patched/esm3_inproc.py",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:41",
+ "seconds": 478.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1536,
+  "max_abs": 8942.5849609375
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.3911045424821484,
+  "rel_change_coord_swap": 0.1052052461015038,
+  "rel_change_seq_shuffle": 0.23244728451209695,
+  "rel_change_rigid_motion": 0.0020265780064980155,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/subcellular_localization/esm_if1/ids_test.txt b/extract/embeddings/subcellular_localization/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm_if1/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/esm_if1/ids_train.txt b/extract/embeddings/subcellular_localization/esm_if1/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm_if1/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/esm_if1/ids_valid.txt b/extract/embeddings/subcellular_localization/esm_if1/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm_if1/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/esm_if1/meta.json b/extract/embeddings/subcellular_localization/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5acc83a9d5e0c63cec7bbb8cc306c47cc7a9217e
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/esm_if1/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "esm_if1",
+ "family": "registry",
+ "target": "esm_if",
+ "weights": "pretrained",
+ "rule": "GVP-Transformer encoder output before decoding",
+ "env": "base",
+ "weights_sha256": "0edb76de890a0108",
+ "n_parameters": 141662150,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:33",
+ "seconds": 633.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 511,
+  "max_abs": 1.4142898321151733
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038823538036952,
+  "rel_change_coord_swap": 0.44554338093155743,
+  "rel_change_seq_shuffle": 3.7119620975877243e-07,
+  "rel_change_rigid_motion": 1.1063191420970738e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/foldseek_3di/ids_test.txt b/extract/embeddings/subcellular_localization/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldseek_3di/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/foldseek_3di/ids_train.txt b/extract/embeddings/subcellular_localization/foldseek_3di/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldseek_3di/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt b/extract/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldseek_3di/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/foldseek_3di/meta.json b/extract/embeddings/subcellular_localization/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..387305a13ac59b41ceabf299d9695e034e58d67c
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldseek_3di/meta.json
@@ -0,0 +1,40 @@
+{
+ "encoder": "foldseek_3di",
+ "family": "patched",
+ "target": "foldseek_3di",
+ "weights": "pretrained",
+ "rule": "one-hot 3Di state per residue; protein level is the state frequency",
+ "env": "base",
+ "tool": "mini3di 0.2.1",
+ "inputs_passed": "N, CA, C, CB coordinates",
+ "n_parameters": 0,
+ "patch": "patched/foldseek_3di.py",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:35",
+ "seconds": 32.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9972,
+  "numerical_rank": 19,
+  "max_abs": 0.9919028282165527
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.7178714286952135,
+  "rel_change_coord_swap": 0.49931369393859204,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/foldvision/ids_test.txt b/extract/embeddings/subcellular_localization/foldvision/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
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diff --git a/extract/embeddings/subcellular_localization/foldvision/ids_train.txt b/extract/embeddings/subcellular_localization/foldvision/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldvision/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/foldvision/ids_valid.txt b/extract/embeddings/subcellular_localization/foldvision/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldvision/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/foldvision/meta.json b/extract/embeddings/subcellular_localization/foldvision/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4b62662b40c58a5d09457c723652c87de4d89aab
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/foldvision/meta.json
@@ -0,0 +1,42 @@
+{
+ "encoder": "foldvision",
+ "family": "patched",
+ "target": "foldvision_global",
+ "weights": "pretrained",
+ "rule": "native FoldVisionEncoder.encode global embedding; no residue states",
+ "env": "base",
+ "checkpoint": "AlexanderKroll/foldvision-encoder",
+ "n_parameters": 122226304,
+ "inputs_passed": "the structure file as given (all atoms present in it), voxelised by FoldVision's own preprocessing",
+ "patch": "patched/foldvision_global.py",
+ "residue_level": false,
+ "pose": "principal-axis pose with fixed axis signs, applied to the structure file before voxelisation",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 06:34",
+ "seconds": 3556.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1024,
+  "max_abs": 5.423613548278809
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.9399117827415466,
+  "rel_change_coord_swap": 0.19160349667072296,
+  "rel_change_seq_shuffle": 0.029323811642825603,
+  "rel_change_rigid_motion": 0.0002744854864431545,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_test.txt b/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_train.txt b/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_valid.txt b/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_pretrained/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_pretrained/meta.json b/extract/embeddings/subcellular_localization/gcpnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c74f2710e205acea34996a3e44f392037eb7284e
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_pretrained/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "gcpnet_pretrained",
+ "family": "patched",
+ "target": "gcpnet_official",
+ "weights": "pretrained",
+ "rule": "official PSR model; 100 scalar channels + 16 vector norms, mean over the heavy atoms of each residue",
+ "env": "base",
+ "checkpoint": "external_repos/GCPNet/checkpoints/PSR/model_epoch_115_localpearson_0_616_localspearman_0_532_localkendall_0_385_globalpearson_0_871_globalspearman_0_869_globalkendall_0_676.ckpt",
+ "checkpoint_sha256": "ff7b73be01fb57d5",
+ "checkpoint_loaded_by": "strict=True",
+ "weights_sha256": "15bd126ac55f26a2",
+ "n_parameters": 1153181,
+ "inputs_passed": "all heavy atoms of the structure file (elements and coordinates); residue identity enters through side-chain atoms",
+ "patch": "patched/gcpnet_official.py",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:27",
+ "seconds": 1013.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 115,
+  "max_abs": 2.0432467460632324
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.545786440372467,
+  "rel_change_coord_swap": 0.26095230877399445,
+  "rel_change_seq_shuffle": 0.03569234535098076,
+  "rel_change_rigid_motion": 0.0002571470904513262,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/subcellular_localization/gcpnet_random/ids_test.txt b/extract/embeddings/subcellular_localization/gcpnet_random/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_random/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_random/ids_train.txt b/extract/embeddings/subcellular_localization/gcpnet_random/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_random/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_random/ids_valid.txt b/extract/embeddings/subcellular_localization/gcpnet_random/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_random/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/gcpnet_random/meta.json b/extract/embeddings/subcellular_localization/gcpnet_random/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..ee44e185395c0032018b39b1f7a305d6b7e087d5
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gcpnet_random/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "gcpnet_random",
+ "family": "patched",
+ "target": "gcpnet_official_random",
+ "weights": "random",
+ "rule": "official architecture, random weights; 100 scalar channels + 16 vector norms per residue",
+ "env": "base",
+ "checkpoint": null,
+ "checkpoint_sha256": null,
+ "checkpoint_loaded_by": "none (random weights, fixed seed)",
+ "weights_sha256": "cdec9adf86f7cd39",
+ "n_parameters": 1153181,
+ "inputs_passed": "all heavy atoms of the structure file (elements and coordinates); residue identity enters through side-chain atoms",
+ "patch": "patched/gcpnet_official.py",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:23",
+ "seconds": 1133.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 116,
+  "max_abs": 2.0826101303100586
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.06854108348488808,
+  "rel_change_coord_swap": 0.0053557404316961765,
+  "rel_change_seq_shuffle": 0.0014149958733469248,
+  "rel_change_rigid_motion": 1.3332899470697157e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/gearnet/ids_test.txt b/extract/embeddings/subcellular_localization/gearnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/gearnet/ids_train.txt b/extract/embeddings/subcellular_localization/gearnet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/gearnet/ids_valid.txt b/extract/embeddings/subcellular_localization/gearnet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/gearnet/meta.json b/extract/embeddings/subcellular_localization/gearnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3f61f98c33afc7eadd23a35e658706e95c690b70
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "gearnet",
+ "family": "registry",
+ "target": "gearnet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "c0af89eafe340139",
+ "n_parameters": 6641408,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:04",
+ "seconds": 45.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 511,
+  "max_abs": 3.4870450496673584
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.05966170943530161,
+  "rel_change_coord_swap": 0.0903857713791805,
+  "rel_change_seq_shuffle": 0.2058370455057908,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_test.txt b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_train.txt b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/gearnet_pretrained/meta.json b/extract/embeddings/subcellular_localization/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2ea9654309ebac56efa13518fcbe05872b4f3a06
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/gearnet_pretrained/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-20 06:18",
+ "seconds": 4171.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 512,
+  "max_abs": 1107.975830078125
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126985494110313,
+  "rel_change_coord_swap": 0.8348704088209604,
+  "rel_change_seq_shuffle": 0.9662572724866123,
+  "rel_change_rigid_motion": 1.2232036816523465e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/subcellular_localization/ipa/ids_test.txt b/extract/embeddings/subcellular_localization/ipa/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/ipa/ids_train.txt b/extract/embeddings/subcellular_localization/ipa/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/ipa/ids_valid.txt b/extract/embeddings/subcellular_localization/ipa/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/ipa/meta.json b/extract/embeddings/subcellular_localization/ipa/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5861dafe546c9f79ccd21d99ea59ac3a9b1fef1f
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "ipa",
+ "family": "registry",
+ "target": "ipa",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues; input in canonical pose",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "e78c71b9309a3464",
+ "n_parameters": 648016,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:03",
+ "seconds": 28.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 1.567211627960205
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.12257404373741311,
+  "rel_change_coord_swap": 0.05155513016107964,
+  "rel_change_seq_shuffle": 0.0797983617810485,
+  "rel_change_rigid_motion": 3.31945237267748e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/ipa_pretrained/ids_test.txt b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/ipa_pretrained/ids_train.txt b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa_pretrained/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/ipa_pretrained/meta.json b/extract/embeddings/subcellular_localization/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..7092ffebb69b7876882c8bc9867cf785bb60405c
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ipa_pretrained/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "2026-09-20 05:10",
+ "seconds": 27.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 128,
+  "max_abs": 0.9746413826942444
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.35788751735660557,
+  "rel_change_coord_swap": 0.3508906219834083,
+  "rel_change_seq_shuffle": 0.22938644958192494,
+  "rel_change_rigid_motion": 4.454701839092521e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/subcellular_localization/pottsmpnn/ids_test.txt b/extract/embeddings/subcellular_localization/pottsmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn/ids_train.txt b/extract/embeddings/subcellular_localization/pottsmpnn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn/ids_valid.txt b/extract/embeddings/subcellular_localization/pottsmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn/meta.json b/extract/embeddings/subcellular_localization/pottsmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..160910c24191379b0cb56a63ee8724fb65d1fe5e
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "pottsmpnn",
+ "family": "registry",
+ "target": "pottsmpnn",
+ "weights": "random",
+ "rule": "encoder h_V after 3 layers, masked mean",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "fd9636d73a1e9994",
+ "n_parameters": 1712085,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:06",
+ "seconds": 43.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 3.3215062618255615
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.07189607480629943,
+  "rel_change_coord_swap": 0.06452992568345384,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.150863828075338e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_test.txt b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_train.txt b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a5e4c2da09ca01713e0ba30d7fcdbe2d508944ee
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_pretrained/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_pretrained",
+ "family": "registry",
+ "target": "pottsmpnn_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "1cfd2bd3bed04f09",
+ "n_parameters": 1712085,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:07",
+ "seconds": 43.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 3.322645664215088
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6454550569687352,
+  "rel_change_coord_swap": 0.12076814557594767,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.1436842851380084e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_test.txt b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_train.txt b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_valid.txt b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/pottsmpnn_soluble/meta.json b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0877fdc4c7ed4e8b49543b0abee8d4afca82c270
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/pottsmpnn_soluble/meta.json
@@ -0,0 +1,38 @@
+{
+ "encoder": "pottsmpnn_soluble",
+ "family": "registry",
+ "target": "pottsmpnn_soluble_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V, masked mean",
+ "env": "base",
+ "weights_sha256": "31f0aac7f4cefa1a",
+ "n_parameters": 1712085,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:08",
+ "seconds": 43.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 2.0122992992401123
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6675711994212048,
+  "rel_change_coord_swap": 0.17917227338286784,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 1.4140547445011483e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/prostt5/ids_test.txt b/extract/embeddings/subcellular_localization/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/prostt5/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/prostt5/ids_train.txt b/extract/embeddings/subcellular_localization/prostt5/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/prostt5/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/prostt5/ids_valid.txt b/extract/embeddings/subcellular_localization/prostt5/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/prostt5/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/prostt5/meta.json b/extract/embeddings/subcellular_localization/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..178b00c304c08d91c62dacd11e3e3067ca9c9f58
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/prostt5/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "prostt5",
+ "family": "hf_plm",
+ "target": "Rostlab/ProstT5",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues; amino-acid track with the <AA2fold> prefix, no 3Di input",
+ "env": "base",
+ "checkpoint": "Rostlab/ProstT5",
+ "checkpoint_revision": "d7d097d5bf9a993ab8f68488b4681d6ca70db9e5",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208164352,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:03",
+ "seconds": 220.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1024,
+  "max_abs": 1.32839834690094
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.5110924480134234,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/protbert_bfd/ids_test.txt b/extract/embeddings/subcellular_localization/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/protbert_bfd/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/protbert_bfd/ids_train.txt b/extract/embeddings/subcellular_localization/protbert_bfd/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/protbert_bfd/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt b/extract/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/protbert_bfd/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/protbert_bfd/meta.json b/extract/embeddings/subcellular_localization/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2ab810fe2463b4d5211f56e9a2cad90c582d02d9
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/protbert_bfd/meta.json
@@ -0,0 +1,43 @@
+{
+ "encoder": "protbert_bfd",
+ "family": "hf_plm",
+ "target": "Rostlab/prot_bert_bfd",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "Rostlab/prot_bert_bfd",
+ "checkpoint_revision": "6c5c8a55a52ff08a664dfd584aa1773f125a0487",
+ "dtype": "float32",
+ "hidden_size": 1024,
+ "n_layers": 30,
+ "n_parameters": 418881536,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 04:47",
+ "seconds": 146.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1023,
+  "max_abs": 2.247859477996826
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.4072423163663681,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/proteinmpnn/ids_test.txt b/extract/embeddings/subcellular_localization/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/proteinmpnn/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/proteinmpnn/ids_train.txt b/extract/embeddings/subcellular_localization/proteinmpnn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/proteinmpnn/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt b/extract/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/proteinmpnn/ids_valid.txt
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diff --git a/extract/embeddings/subcellular_localization/proteinmpnn/meta.json b/extract/embeddings/subcellular_localization/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..3d87c594d443b1828acc3b1400345985be5b4633
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/proteinmpnn/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "proteinmpnn",
+ "family": "registry",
+ "target": "proteinmpnn_pretrained",
+ "weights": "pretrained",
+ "rule": "encoder h_V after 3 encoder layers, before the decoder",
+ "env": "base",
+ "checkpoint": "checkpoints/proteinmpnn_v48_020.pt",
+ "checkpoint_sha256": "c9cb4a671d796041",
+ "checkpoint_loaded_by": "wrapper load_pretrained()",
+ "weights_sha256": "01d6f9d31117f274",
+ "n_parameters": 1660485,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:07",
+ "seconds": 38.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 2.2541322708129883
+ },
+ "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/extract/embeddings/subcellular_localization/ref_composition/ids_test.txt b/extract/embeddings/subcellular_localization/ref_composition/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ref_composition/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/ref_composition/ids_train.txt b/extract/embeddings/subcellular_localization/ref_composition/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ref_composition/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/ref_composition/ids_valid.txt b/extract/embeddings/subcellular_localization/ref_composition/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ref_composition/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/ref_composition/meta.json b/extract/embeddings/subcellular_localization/ref_composition/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..b136c9db0c161808c1326d621781510cea8e30e6
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/ref_composition/meta.json
@@ -0,0 +1,18 @@
+{
+ "encoder": "ref_composition",
+ "family": "non-learned reference",
+ "weights": "none",
+ "n_parameters": 0,
+ "rule": "20 amino-acid frequencies, log length, length/600, fraction outside the 20-letter alphabet",
+ "inputs_passed": "amino-acid sequence only",
+ "hidden_size": 23,
+ "task": "subcellular_localization",
+ "ids_copied_from": "esm2_150m",
+ "n_per_split": {
+  "train": 6000,
+  "valid": 1500,
+  "test": 2473
+ },
+ "purpose": "downstream floor: what the task scores without any learned representation",
+ "date": "2026-09-21 14:00"
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/saprot/ids_test.txt b/extract/embeddings/subcellular_localization/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/saprot/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/saprot/ids_train.txt b/extract/embeddings/subcellular_localization/saprot/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/saprot/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/saprot/ids_valid.txt b/extract/embeddings/subcellular_localization/saprot/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/saprot/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/saprot/meta.json b/extract/embeddings/subcellular_localization/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..aef26176111da41f27bc7c763cae81232e273e46
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/saprot/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "saprot",
+ "family": "patched",
+ "target": "saprot_hf",
+ "weights": "pretrained",
+ "rule": "final hidden states at the L residue positions of AA+3Di tokens",
+ "env": "base",
+ "checkpoint": "westlake-repl/SaProt_650M_AF2",
+ "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38",
+ "n_parameters": 651242901,
+ "inputs_passed": "amino-acid track: real sequence; 3Di track: real tokens from mini3di on the structure; no pLDDT masking",
+ "patch": "patched/saprot_hf.py",
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:34",
+ "seconds": 454.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 1279,
+  "max_abs": 1.595617651939392
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.8705030813272382,
+  "rel_change_coord_swap": 0.4102216970171252,
+  "rel_change_seq_shuffle": 0.8413755808217256,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/schnet/ids_test.txt b/extract/embeddings/subcellular_localization/schnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/schnet/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/schnet/ids_train.txt b/extract/embeddings/subcellular_localization/schnet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/schnet/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/schnet/ids_valid.txt b/extract/embeddings/subcellular_localization/schnet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/schnet/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/schnet/meta.json b/extract/embeddings/subcellular_localization/schnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..840101ceb8f953f862ebf90f61d83af6f44d8b42
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/schnet/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "schnet",
+ "family": "registry",
+ "target": "schnet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "a554781da0916f60",
+ "n_parameters": 244480,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:01",
+ "seconds": 64.8,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 1.3691208362579346
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.024272346150889114,
+  "rel_change_coord_swap": 0.04067997024144254,
+  "rel_change_seq_shuffle": 0.0926744111105295,
+  "rel_change_rigid_motion": 1.4309623780125316e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/tfn/ids_test.txt b/extract/embeddings/subcellular_localization/tfn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn/ids_test.txt
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diff --git a/extract/embeddings/subcellular_localization/tfn/ids_train.txt b/extract/embeddings/subcellular_localization/tfn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/tfn/ids_valid.txt b/extract/embeddings/subcellular_localization/tfn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/tfn/meta.json b/extract/embeddings/subcellular_localization/tfn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..2bfa3f96a24571ddc6e1e487433da816bf7f14ce
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn/meta.json
@@ -0,0 +1,39 @@
+{
+ "encoder": "tfn",
+ "family": "registry",
+ "target": "tfn",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "seed": 20260919,
+ "weights_sha256": "b07ce6d9887ef8db",
+ "n_parameters": 250880,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:02",
+ "seconds": 103.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 127,
+  "max_abs": 3.697178840637207
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.035918465297843816,
+  "rel_change_coord_swap": 0.08890221178385639,
+  "rel_change_seq_shuffle": 0.15717389464953313,
+  "rel_change_rigid_motion": 1.0772144824293731e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/subcellular_localization/tfn_pretrained/ids_test.txt b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d32ab23ef3c81176bdd4f24f276b62fb65f254a
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_test.txt
@@ -0,0 +1,2473 @@
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diff --git a/extract/embeddings/subcellular_localization/tfn_pretrained/ids_train.txt b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fdb1cb1696b080f70f8b82d9323534b828dbfe3
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_train.txt
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diff --git a/extract/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3e555ebf7179bfae258726eeb048681f54a0958
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn_pretrained/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/subcellular_localization/tfn_pretrained/meta.json b/extract/embeddings/subcellular_localization/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a0911d77e6bc013195a314215b1bb783dd9b5b7f
--- /dev/null
+++ b/extract/embeddings/subcellular_localization/tfn_pretrained/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "tfn_pretrained",
+ "family": "registry",
+ "target": "tfn_pretrained",
+ "weights": "pretrained",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "checkpoints/tfn_pretrained/best.pt",
+ "checkpoint_sha256": "17af58de61a4674c",
+ "checkpoint_loaded_by": "strict load of 'encoder_state': 39 of 39 tensors",
+ "weights_sha256": "a7afc00e258bf380",
+ "n_parameters": 250880,
+ "task": "subcellular_localization",
+ "date": "2026-09-20 05:09",
+ "seconds": 24.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/subcellular_localization.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 2473,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 9973,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 9973,
+  "numerical_rank": 107,
+  "max_abs": 1.805875301361084
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.038222533247724046,
+  "rel_change_coord_swap": 0.0726356100068006,
+  "rel_change_seq_shuffle": 0.2809558822048089,
+  "rel_change_rigid_motion": 9.074813202694072e-08,
+  "verdict": "pass"
+ }
+}