diff --git a/extract/embeddings/membrane_soluble/cdconv/ids_test.txt b/extract/embeddings/membrane_soluble/cdconv/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/cdconv/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/cdconv/ids_train.txt b/extract/embeddings/membrane_soluble/cdconv/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/cdconv/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/cdconv/ids_valid.txt b/extract/embeddings/membrane_soluble/cdconv/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/cdconv/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/cdconv/meta.json b/extract/embeddings/membrane_soluble/cdconv/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..48ed07fd39cc470a7c167fd3eb9e48fe8b34d122
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:26",
+ "seconds": 248.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 256,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 256,
+  "max_abs": 0.22332660853862762
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0015725420671515167,
+  "rel_change_coord_swap": 0.011715239379554987,
+  "rel_change_seq_shuffle": 0.00444194907322526,
+  "rel_change_rigid_motion": 7.286431369379898e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/dimenet/ids_test.txt b/extract/embeddings/membrane_soluble/dimenet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/dimenet/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/dimenet/ids_train.txt b/extract/embeddings/membrane_soluble/dimenet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/dimenet/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/dimenet/ids_valid.txt b/extract/embeddings/membrane_soluble/dimenet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/dimenet/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/dimenet/meta.json b/extract/embeddings/membrane_soluble/dimenet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..76bac2ab2547c40b165646268304c9f41ca823f4
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:19",
+ "seconds": 30.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.9204307794570923
+ },
+ "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/membrane_soluble/esm1b/ids_test.txt b/extract/embeddings/membrane_soluble/esm1b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm1b/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm1b/ids_train.txt b/extract/embeddings/membrane_soluble/esm1b/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm1b/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm1b/ids_valid.txt b/extract/embeddings/membrane_soluble/esm1b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm1b/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm1b/meta.json b/extract/embeddings/membrane_soluble/esm1b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..186aa57e1cdc6d7499c3d5fcd69e6e0feb1830a7
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 15:57",
+ "seconds": 258.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 17.943994522094727
+ },
+ "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/membrane_soluble/esm2_150m/ids_test.txt b/extract/embeddings/membrane_soluble/esm2_150m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_150m/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_150m/ids_train.txt b/extract/embeddings/membrane_soluble/esm2_150m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_150m/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_150m/ids_valid.txt b/extract/embeddings/membrane_soluble/esm2_150m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_150m/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_150m/meta.json b/extract/embeddings/membrane_soluble/esm2_150m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..049b5ab648cf80e6ea5bad501c4d4eb332e4f07c
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:05",
+ "seconds": 139.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 640,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 639,
+  "max_abs": 7.350792407989502
+ },
+ "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/membrane_soluble/esm2_35m/ids_test.txt b/extract/embeddings/membrane_soluble/esm2_35m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_35m/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_35m/ids_train.txt b/extract/embeddings/membrane_soluble/esm2_35m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_35m/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_35m/ids_valid.txt b/extract/embeddings/membrane_soluble/esm2_35m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_35m/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_35m/meta.json b/extract/embeddings/membrane_soluble/esm2_35m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..05a189d399f97bbfbc25c6d1df09178109a0a5d0
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:03",
+ "seconds": 32.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 480,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 479,
+  "max_abs": 6.30465841293335
+ },
+ "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/membrane_soluble/esm2_3b/ids_test.txt b/extract/embeddings/membrane_soluble/esm2_3b/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_3b/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_3b/ids_train.txt b/extract/embeddings/membrane_soluble/esm2_3b/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_3b/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_3b/ids_valid.txt b/extract/embeddings/membrane_soluble/esm2_3b/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_3b/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_3b/meta.json b/extract/embeddings/membrane_soluble/esm2_3b/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..624c7e7d6502ff21fe4cb97de71bae2c357a7c30
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:15",
+ "seconds": 597.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 2560,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 2559,
+  "max_abs": 14.548606872558594
+ },
+ "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/membrane_soluble/esm2_650m/ids_test.txt b/extract/embeddings/membrane_soluble/esm2_650m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_650m/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_650m/ids_train.txt b/extract/embeddings/membrane_soluble/esm2_650m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_650m/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_650m/ids_valid.txt b/extract/embeddings/membrane_soluble/esm2_650m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_650m/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_650m/meta.json b/extract/embeddings/membrane_soluble/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..af86add181a3742ef094679663669c325a108baf
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:10",
+ "seconds": 408.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 8.669005393981934
+ },
+ "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/membrane_soluble/esm2_8m/ids_test.txt b/extract/embeddings/membrane_soluble/esm2_8m/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_8m/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_8m/ids_train.txt b/extract/embeddings/membrane_soluble/esm2_8m/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_8m/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm2_8m/ids_valid.txt b/extract/embeddings/membrane_soluble/esm2_8m/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm2_8m/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm2_8m/meta.json b/extract/embeddings/membrane_soluble/esm2_8m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c647171cbef531dd8dea6f23bbbd6b58bf9533f7
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:02",
+ "seconds": 16.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 320,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 319,
+  "max_abs": 5.3099284172058105
+ },
+ "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/membrane_soluble/esm3/ids_test.txt b/extract/embeddings/membrane_soluble/esm3/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm3/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm3/ids_train.txt b/extract/embeddings/membrane_soluble/esm3/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm3/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/esm3/ids_valid.txt b/extract/embeddings/membrane_soluble/esm3/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm3/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm3/meta.json b/extract/embeddings/membrane_soluble/esm3/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..70e5855a97129abd26920e35aef3ed7421803bba
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 18:17",
+ "seconds": 1065.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1536,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "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/membrane_soluble/esm_if1/ids_test.txt b/extract/embeddings/membrane_soluble/esm_if1/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm_if1/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/esm_if1/ids_train.txt b/extract/embeddings/membrane_soluble/esm_if1/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm_if1/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/esm_if1/ids_valid.txt b/extract/embeddings/membrane_soluble/esm_if1/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/esm_if1/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/esm_if1/meta.json b/extract/embeddings/membrane_soluble/esm_if1/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..91a32e7b7111d152548bd013545890eaa383c781
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 17:56",
+ "seconds": 712.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 511,
+  "max_abs": 1.4721933603286743
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 1.5038822793102065,
+  "rel_change_coord_swap": 0.44554341899146355,
+  "rel_change_seq_shuffle": 3.5828770413372914e-07,
+  "rel_change_rigid_motion": 1.1024219872199306e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/foldseek_3di/ids_test.txt b/extract/embeddings/membrane_soluble/foldseek_3di/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldseek_3di/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/foldseek_3di/ids_train.txt b/extract/embeddings/membrane_soluble/foldseek_3di/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldseek_3di/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/foldseek_3di/ids_valid.txt b/extract/embeddings/membrane_soluble/foldseek_3di/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldseek_3di/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/foldseek_3di/meta.json b/extract/embeddings/membrane_soluble/foldseek_3di/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..bf345e3606470472c6b593bedf91af1e0e89499f
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 18:10",
+ "seconds": 91.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 20,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10498,
+  "numerical_rank": 19,
+  "max_abs": 0.9929577708244324
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.7178714286952135,
+  "rel_change_coord_swap": 0.49931369393859204,
+  "rel_change_seq_shuffle": 0.0,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/foldvision/ids_test.txt b/extract/embeddings/membrane_soluble/foldvision/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldvision/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/foldvision/ids_train.txt b/extract/embeddings/membrane_soluble/foldvision/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldvision/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/foldvision/ids_valid.txt b/extract/embeddings/membrane_soluble/foldvision/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/foldvision/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/foldvision/meta.json b/extract/embeddings/membrane_soluble/foldvision/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..c021d6265c5c4452b120e37c836ca2b9fa9fec93
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 20:39",
+ "seconds": 8929.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 5.496109962463379
+ },
+ "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/membrane_soluble/gcpnet_pretrained/ids_test.txt b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_train.txt b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_valid.txt b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_pretrained/meta.json b/extract/embeddings/membrane_soluble/gcpnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..74e36d9462037ff6bedb16962b3c3a1420f07d33
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 17:44",
+ "seconds": 2780.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 115,
+  "max_abs": 2.0493593215942383
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.5457864999771118,
+  "rel_change_coord_swap": 0.26095233857631683,
+  "rel_change_seq_shuffle": 0.03569233417510986,
+  "rel_change_rigid_motion": 0.00025715972878970206,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/membrane_soluble/gcpnet_random/ids_test.txt b/extract/embeddings/membrane_soluble/gcpnet_random/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_random/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_random/ids_train.txt b/extract/embeddings/membrane_soluble/gcpnet_random/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_random/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_random/ids_valid.txt b/extract/embeddings/membrane_soluble/gcpnet_random/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gcpnet_random/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/gcpnet_random/meta.json b/extract/embeddings/membrane_soluble/gcpnet_random/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cfc6fce13d0b87180acb2a20abeb98fe9ba75364
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:53",
+ "seconds": 1853.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 116,
+  "max_abs": 2.0826101303100586
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.06854108348488808,
+  "rel_change_coord_swap": 0.005355739267542958,
+  "rel_change_seq_shuffle": 0.0014150050119496882,
+  "rel_change_rigid_motion": 1.3333202332432847e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/gearnet/ids_test.txt b/extract/embeddings/membrane_soluble/gearnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/gearnet/ids_train.txt b/extract/embeddings/membrane_soluble/gearnet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/gearnet/ids_valid.txt b/extract/embeddings/membrane_soluble/gearnet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/gearnet/meta.json b/extract/embeddings/membrane_soluble/gearnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..331af4c61b48e5a832f0baed79fac5ac7a43e829
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:22",
+ "seconds": 64.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 511,
+  "max_abs": 4.480013370513916
+ },
+ "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/membrane_soluble/gearnet_pretrained/ids_test.txt b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_train.txt b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_valid.txt b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gearnet_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/gearnet_pretrained/meta.json b/extract/embeddings/membrane_soluble/gearnet_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a358c1eea831c4cb27b23e6a79eb798a776fc109
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 17:59",
+ "seconds": 4905.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 512,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 512,
+  "max_abs": 343.0392761230469
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.6126985997279927,
+  "rel_change_coord_swap": 0.834870377166093,
+  "rel_change_seq_shuffle": 0.9662573113499922,
+  "rel_change_rigid_motion": 1.2520495007830443e-07,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/membrane_soluble/gvp/ids_test.txt b/extract/embeddings/membrane_soluble/gvp/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gvp/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/gvp/ids_train.txt b/extract/embeddings/membrane_soluble/gvp/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gvp/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/gvp/ids_valid.txt b/extract/embeddings/membrane_soluble/gvp/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/gvp/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/gvp/meta.json b/extract/embeddings/membrane_soluble/gvp/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..dc0f710b36dd8a27b3a93c3390980f239dfd39ae
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:22",
+ "seconds": 77.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 115,
+  "max_abs": 2.874041795730591
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03118545954140465,
+  "rel_change_coord_swap": 0.006320145062739492,
+  "rel_change_seq_shuffle": 0.002777464971628065,
+  "rel_change_rigid_motion": 8.304387699605636e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/ipa/ids_test.txt b/extract/embeddings/membrane_soluble/ipa/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa/ids_test.txt
@@ -0,0 +1,3000 @@
+Q28165
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diff --git a/extract/embeddings/membrane_soluble/ipa/ids_train.txt b/extract/embeddings/membrane_soluble/ipa/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/ipa/ids_valid.txt b/extract/embeddings/membrane_soluble/ipa/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/ipa/meta.json b/extract/embeddings/membrane_soluble/ipa/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cb6f8a9adea10c7ef0893dff2a2d524daeba7234
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:21",
+ "seconds": 46.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.2452197074890137
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.12257404285458484,
+  "rel_change_coord_swap": 0.05155514046018929,
+  "rel_change_seq_shuffle": 0.0797983365660505,
+  "rel_change_rigid_motion": 3.403308910280915e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/ipa_pretrained/ids_train.txt b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/ipa_pretrained/ids_valid.txt b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ipa_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/ipa_pretrained/meta.json b/extract/embeddings/membrane_soluble/ipa_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..02096c250ff9245f43ae85a10e493c7993146eb5
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:57",
+ "seconds": 139.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 128,
+  "max_abs": 1.0335500240325928
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.35788752838037763,
+  "rel_change_coord_swap": 0.3508906190490385,
+  "rel_change_seq_shuffle": 0.22938682807551403,
+  "rel_change_rigid_motion": 4.295811789516891e-06,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/membrane_soluble/mace/ids_test.txt b/extract/embeddings/membrane_soluble/mace/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/mace/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/mace/ids_train.txt b/extract/embeddings/membrane_soluble/mace/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/mace/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/mace/ids_valid.txt b/extract/embeddings/membrane_soluble/mace/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/mace/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/mace/meta.json b/extract/embeddings/membrane_soluble/mace/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..46a760e3ba0e21763ae760ed7aceec23c037fac7
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:21",
+ "seconds": 40.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.7183618545532227
+ },
+ "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/membrane_soluble/pottsmpnn/ids_test.txt b/extract/embeddings/membrane_soluble/pottsmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn/ids_train.txt b/extract/embeddings/membrane_soluble/pottsmpnn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn/ids_valid.txt b/extract/embeddings/membrane_soluble/pottsmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn/meta.json b/extract/embeddings/membrane_soluble/pottsmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..8dc9e2feba02d369d52e703785aab6223c90ac30
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:28",
+ "seconds": 122.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 3.334198236465454
+ },
+ "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/membrane_soluble/pottsmpnn_ft/ids_test.txt b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_train.txt b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_valid.txt b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_ft/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_ft/meta.json b/extract/embeddings/membrane_soluble/pottsmpnn_ft/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5c118de76699c09f5413ba29734b4f1271e6dcc2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:38",
+ "seconds": 131.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.580057144165039
+ },
+ "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/membrane_soluble/pottsmpnn_pretrained/ids_test.txt b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_train.txt b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_valid.txt b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/meta.json b/extract/embeddings/membrane_soluble/pottsmpnn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a1be18bcbdc44938712477dd94ba0640f0a35662
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:33",
+ "seconds": 147.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "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/membrane_soluble/pottsmpnn_soluble/ids_test.txt b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_train.txt b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_valid.txt b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/pottsmpnn_soluble/meta.json b/extract/embeddings/membrane_soluble/pottsmpnn_soluble/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..843af17cdb292f6943b88332dcd9090e505ea8fd
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:35",
+ "seconds": 149.5,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.9480880498886108
+ },
+ "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/membrane_soluble/prostt5/ids_test.txt b/extract/embeddings/membrane_soluble/prostt5/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prostt5/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/prostt5/ids_train.txt b/extract/embeddings/membrane_soluble/prostt5/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prostt5/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/prostt5/ids_valid.txt b/extract/embeddings/membrane_soluble/prostt5/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prostt5/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/prostt5/meta.json b/extract/embeddings/membrane_soluble/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..e36c3585a8ee226558fc8c0d5b6504c818c92f17
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:19",
+ "seconds": 223.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 1.328553557395935
+ },
+ "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/membrane_soluble/protbert_bfd/ids_test.txt b/extract/embeddings/membrane_soluble/protbert_bfd/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/protbert_bfd/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/protbert_bfd/ids_train.txt b/extract/embeddings/membrane_soluble/protbert_bfd/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/protbert_bfd/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/protbert_bfd/ids_valid.txt b/extract/embeddings/membrane_soluble/protbert_bfd/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/protbert_bfd/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/protbert_bfd/meta.json b/extract/embeddings/membrane_soluble/protbert_bfd/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..90b52a2ad05e6cddb100c3e0ea61c415d169be51
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:02",
+ "seconds": 91.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "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/membrane_soluble/proteinmpnn/ids_test.txt b/extract/embeddings/membrane_soluble/proteinmpnn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/proteinmpnn/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/proteinmpnn/ids_train.txt b/extract/embeddings/membrane_soluble/proteinmpnn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/proteinmpnn/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/proteinmpnn/ids_valid.txt b/extract/embeddings/membrane_soluble/proteinmpnn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/proteinmpnn/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/proteinmpnn/meta.json b/extract/embeddings/membrane_soluble/proteinmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..0466b80959e85f15e1145ef432f088865f5b5ca5
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:30",
+ "seconds": 122.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 2.2565181255340576
+ },
+ "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/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_train.txt b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_valid.txt b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/meta.json b/extract/embeddings/membrane_soluble/prottrans_t5_xl_u50/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..6d73fad69d02582a58ef322ed64f83eb21307523
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:00",
+ "seconds": 187.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1024,
+  "max_abs": 0.6457812190055847
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0,
+  "rel_change_coord_swap": 0.0,
+  "rel_change_seq_shuffle": 0.7503630666663541,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/ref_composition/ids_test.txt b/extract/embeddings/membrane_soluble/ref_composition/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ref_composition/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/ref_composition/ids_train.txt b/extract/embeddings/membrane_soluble/ref_composition/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ref_composition/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/ref_composition/ids_valid.txt b/extract/embeddings/membrane_soluble/ref_composition/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/ref_composition/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/ref_composition/meta.json b/extract/embeddings/membrane_soluble/ref_composition/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5ded1a021a74bd80c331c3fa6d9b97fa12cd61b9
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "ids_copied_from": "esm2_150m",
+ "n_per_split": {
+  "train": 6000,
+  "valid": 1500,
+  "test": 3000
+ },
+ "purpose": "downstream floor: what the task scores without any learned representation",
+ "date": "2026-09-21 14:00"
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/saprot/ids_test.txt b/extract/embeddings/membrane_soluble/saprot/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/saprot/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/saprot/ids_train.txt b/extract/embeddings/membrane_soluble/saprot/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/saprot/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/saprot/ids_valid.txt b/extract/embeddings/membrane_soluble/saprot/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/saprot/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/saprot/meta.json b/extract/embeddings/membrane_soluble/saprot/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..208bbbe8d1ade2e4805e2ac53d9152e081295e60
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 18:08",
+ "seconds": 766.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 1279,
+  "max_abs": 2.203648805618286
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.8705030813272382,
+  "rel_change_coord_swap": 0.4102216970171252,
+  "rel_change_seq_shuffle": 0.8413755808217256,
+  "rel_change_rigid_motion": 0.0,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/schnet/ids_test.txt b/extract/embeddings/membrane_soluble/schnet/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/schnet/ids_test.txt
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diff --git a/extract/embeddings/membrane_soluble/schnet/ids_train.txt b/extract/embeddings/membrane_soluble/schnet/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/schnet/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/schnet/ids_valid.txt b/extract/embeddings/membrane_soluble/schnet/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/schnet/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/schnet/meta.json b/extract/embeddings/membrane_soluble/schnet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..4b64ce6dccb074f5d8aa18b2bc2096ad4cc56817
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:17",
+ "seconds": 65.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 1.629762887954712
+ },
+ "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/membrane_soluble/tfn/ids_test.txt b/extract/embeddings/membrane_soluble/tfn/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/tfn/ids_train.txt b/extract/embeddings/membrane_soluble/tfn/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn/ids_train.txt
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diff --git a/extract/embeddings/membrane_soluble/tfn/ids_valid.txt b/extract/embeddings/membrane_soluble/tfn/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn/ids_valid.txt
@@ -0,0 +1,1500 @@
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diff --git a/extract/embeddings/membrane_soluble/tfn/meta.json b/extract/embeddings/membrane_soluble/tfn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..f2c18e0b8dff8f79463a7a7b196a6dc475dadd7c
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:18",
+ "seconds": 104.9,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 127,
+  "max_abs": 3.5326552391052246
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.035918458146980324,
+  "rel_change_coord_swap": 0.0889021986269148,
+  "rel_change_seq_shuffle": 0.15717390041969298,
+  "rel_change_rigid_motion": 1.0301484224666915e-07,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_test.txt
@@ -0,0 +1,3000 @@
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diff --git a/extract/embeddings/membrane_soluble/tfn_pretrained/ids_train.txt b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_train.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_train.txt
@@ -0,0 +1,6000 @@
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diff --git a/extract/embeddings/membrane_soluble/tfn_pretrained/ids_valid.txt b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_valid.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad501c73f0a1855d3d6decdb16a0fe4397c5b1f2
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/tfn_pretrained/ids_valid.txt
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diff --git a/extract/embeddings/membrane_soluble/tfn_pretrained/meta.json b/extract/embeddings/membrane_soluble/tfn_pretrained/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..652d9facf367dd6a730dae2b1df257d9be527049
--- /dev/null
+++ b/extract/embeddings/membrane_soluble/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": "membrane_soluble",
+ "date": "2026-09-20 16:55",
+ "seconds": 103.7,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/membrane_soluble.csv",
+ "rows": "stage1 == 1",
+ "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)",
+ "n_per_split": {
+  "test": 3000,
+  "train": 6000,
+  "valid": 1500
+ },
+ "health": {
+  "n_rows": 10500,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 10500,
+  "numerical_rank": 108,
+  "max_abs": 1.8231700658798218
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.03822254381723404,
+  "rel_change_coord_swap": 0.07263561021148568,
+  "rel_change_seq_shuffle": 0.28095588441393055,
+  "rel_change_rigid_motion": 9.598232694941571e-08,
+  "verdict": "pass"
+ }
+}
diff --git a/extract/embeddings/ppi_affinity/ankh_base/ids_chains.txt b/extract/embeddings/ppi_affinity/ankh_base/ids_chains.txt
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index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
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diff --git a/extract/embeddings/ppi_affinity/ankh_base/meta.json b/extract/embeddings/ppi_affinity/ankh_base/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..a3db1a59d949dbe33ac6d8bd01a8c1c5b015e51f
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/ankh_base/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "ankh_base",
+ "family": "hf_plm",
+ "target": "ElnaggarLab/ankh-base",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "ElnaggarLab/ankh-base",
+ "checkpoint_revision": "d99cb6b966530dfc2ae96bc69d9255c2a07308b0",
+ "dtype": "float32",
+ "hidden_size": 768,
+ "n_layers": 48,
+ "n_parameters": 453170688,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "ppi_affinity",
+ "date": "2026-09-19 18:55",
+ "seconds": 34.2,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 768,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 763,
+  "max_abs": 0.7802026271820068
+ },
+ "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/ppi_affinity/cdconv/ids_chains.txt b/extract/embeddings/ppi_affinity/cdconv/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/cdconv/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/cdconv/meta.json b/extract/embeddings/ppi_affinity/cdconv/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5b0350ac4869a1d81a559bf8aad0127ab6edf3f3
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/cdconv/meta.json
@@ -0,0 +1,37 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 19:00",
+ "seconds": 313.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 256,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 253,
+  "max_abs": 0.19885845482349396
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.0015725446282885969,
+  "rel_change_coord_swap": 0.011715235188603401,
+  "rel_change_seq_shuffle": 0.004441953031346202,
+  "rel_change_rigid_motion": 7.20397750342272e-08,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/ppi_affinity/dimenet/ids_chains.txt b/extract/embeddings/ppi_affinity/dimenet/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
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diff --git a/extract/embeddings/ppi_affinity/dimenet/meta.json b/extract/embeddings/ppi_affinity/dimenet/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..839305fbbb9b512b5a9a1d87c1eed290d6946f92
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/dimenet/meta.json
@@ -0,0 +1,37 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 18:49",
+ "seconds": 11.1,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 127,
+  "max_abs": 0.8631141185760498
+ },
+ "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/ppi_affinity/esm2_150m/ids_chains.txt b/extract/embeddings/ppi_affinity/esm2_150m/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_150m/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/esm2_150m/meta.json b/extract/embeddings/ppi_affinity/esm2_150m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..cb5dac5bc4107201b450914325ad713ccef26a1c
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_150m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 18:44",
+ "seconds": 10.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 640,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 639,
+  "max_abs": 7.13456916809082
+ },
+ "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/ppi_affinity/esm2_650m/ids_chains.txt b/extract/embeddings/ppi_affinity/esm2_650m/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_650m/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/esm2_650m/meta.json b/extract/embeddings/ppi_affinity/esm2_650m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..25d1f676280569a5f315a97dc2155d56d930eda4
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_650m/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "esm2_650m",
+ "family": "hf_plm",
+ "target": "facebook/esm2_t33_650M_UR50D",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues",
+ "env": "base",
+ "checkpoint": "facebook/esm2_t33_650M_UR50D",
+ "checkpoint_revision": "08e4846e537177426273712802403f7ba8261b6c",
+ "dtype": "float32",
+ "hidden_size": 1280,
+ "n_layers": 33,
+ "n_parameters": 650714261,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "ppi_affinity",
+ "date": "2026-09-19 18:46",
+ "seconds": 25.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 1280,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 1279,
+  "max_abs": 8.617515563964844
+ },
+ "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/ppi_affinity/esm2_8m/ids_chains.txt b/extract/embeddings/ppi_affinity/esm2_8m/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_8m/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/esm2_8m/meta.json b/extract/embeddings/ppi_affinity/esm2_8m/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..073fe4b43c1a018d4661845ed585eb9c9424b5d1
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/esm2_8m/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 18:42",
+ "seconds": 3.4,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 320,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 319,
+  "max_abs": 5.320175647735596
+ },
+ "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/ppi_affinity/gcpnet_random/ids_chains.txt b/extract/embeddings/ppi_affinity/gcpnet_random/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/gcpnet_random/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/gcpnet_random/meta.json b/extract/embeddings/ppi_affinity/gcpnet_random/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..9c506823779d34fc316f2587b88ea711c9ea6f08
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/gcpnet_random/meta.json
@@ -0,0 +1,41 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 20:29",
+ "seconds": 162.6,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 116,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 116,
+  "max_abs": 2.0643062591552734
+ },
+ "input_audit": {
+  "rel_change_jitter_1A": 0.06854108721017838,
+  "rel_change_coord_swap": 0.005355729255825281,
+  "rel_change_seq_shuffle": 0.001415007165633142,
+  "rel_change_rigid_motion": 1.3346775631362107e-05,
+  "verdict": "pass"
+ }
+}
\ No newline at end of file
diff --git a/extract/embeddings/ppi_affinity/pottsmpnn/ids_chains.txt b/extract/embeddings/ppi_affinity/pottsmpnn/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/pottsmpnn/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/pottsmpnn/meta.json b/extract/embeddings/ppi_affinity/pottsmpnn/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..5bc84c9ce867837e13a1f1ab6a406eb5116b1bb6
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/pottsmpnn/meta.json
@@ -0,0 +1,37 @@
+{
+ "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": "ppi_affinity",
+ "date": "2026-09-19 19:15",
+ "seconds": 41.3,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 128,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 127,
+  "max_abs": 2.9866631031036377
+ },
+ "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/ppi_affinity/prostt5/ids_chains.txt b/extract/embeddings/ppi_affinity/prostt5/ids_chains.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/prostt5/ids_chains.txt
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diff --git a/extract/embeddings/ppi_affinity/prostt5/meta.json b/extract/embeddings/ppi_affinity/prostt5/meta.json
new file mode 100644
index 0000000000000000000000000000000000000000..57337857452ff67998a07858082aa2e7eb8188ee
--- /dev/null
+++ b/extract/embeddings/ppi_affinity/prostt5/meta.json
@@ -0,0 +1,41 @@
+{
+ "encoder": "prostt5",
+ "family": "hf_plm",
+ "target": "Rostlab/ProstT5",
+ "weights": "pretrained",
+ "rule": "final residue states, special tokens removed, masked mean over valid residues; amino-acid track with the <AA2fold> prefix, no 3Di input",
+ "env": "base",
+ "checkpoint": "Rostlab/ProstT5",
+ "checkpoint_revision": "d7d097d5bf9a993ab8f68488b4681d6ca70db9e5",
+ "dtype": "float16",
+ "hidden_size": 1024,
+ "n_layers": 24,
+ "n_parameters": 1208164352,
+ "inputs_passed": "amino-acid sequence only",
+ "task": "ppi_affinity",
+ "date": "2026-09-19 19:04",
+ "seconds": 37.0,
+ "pooling": "masked mean over all residues of the chain",
+ "manifest": "manifest/ppi_affinity.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": {
+  "chains": 2589
+ },
+ "health": {
+  "n_rows": 2589,
+  "dim": 1024,
+  "nan_values": 0,
+  "all_zero_rows": 0,
+  "distinct_rows": 2589,
+  "numerical_rank": 1022,
+  "max_abs": 1.3355034589767456
+ },
+ "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