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probing_embeddings/dimenet/meta.json

@@ -0,0 +1,33 @@
+{
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+ "target": "dimenet",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
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+ "seed": 20260919,
+ "weights_sha256": "71e5f811f644cdf2",
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+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:28",
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+ "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5",
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+}

probing_embeddings/esm2_150m/meta.json

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+{
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+  "hub_id": "facebook/esm2_t30_150M_UR50D",
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+  "input": "sequence of the residues kept in labels.h5; discontinuous CATH domains are passed as one concatenated sequence",
+  "rows": "identical to residue/* rows of probing_data/labels.h5",
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+  "date": "2026-09-19"
+}

probing_embeddings/esm2_650m/meta.json

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+{
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+  "input": "sequence of the residues kept in labels.h5; discontinuous CATH domains are passed as one concatenated sequence",
+  "rows": "identical to residue/* rows of probing_data/labels.h5",
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+  "date": "2026-09-19"
+}

probing_embeddings/esm3/meta.json

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+{
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+ "target": "esm3_inproc",
+ "weights": "pretrained",
+ "rule": "final trunk residue embeddings, sequence and structure tracks",
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+ "checkpoint": "esm3-sm-open-v1/data/weights/esm3_sm_open_v1.pth",
+ "dtype": "bfloat16",
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+ "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",
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 19:41",
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+ }
+}

probing_embeddings/esm_if1/meta.json

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+{
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+ "family": "registry",
+ "target": "esm_if",
+ "weights": "pretrained",
+ "rule": "GVP-Transformer encoder output before decoding",
+ "env": "base",
+ "weights_sha256": "0edb76de890a0108",
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+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:26",
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+ "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5",
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+ }
+}

probing_embeddings/foldseek_3di/meta.json

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+{
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+ "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",
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:50",
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+ }
+}

probing_embeddings/foldvision/meta.json

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+{
+ "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",
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 19:49",
+ "seconds": 2770.2,
+ "n_domains": 19461,
+ "dim": 1024,
+ "pooled_only": true,
+ "row_convention": "row r of pooled_fp32.npy is row r of protein/* in labels.h5; no residue states, so only the protein-level probes apply",
+ "health": {
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+ }
+}

probing_embeddings/gearnet/meta.json

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+{
+ "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",
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+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 18:34",
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+  "verdict": "pass"
+ }
+}

probing_embeddings/gearnet_pretrained/meta.json

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+{
+ "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",
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+ "dataset": "protcompass/probing_data/labels.h5",
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+}

probing_embeddings/pottsmpnn/meta.json

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+{
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+ "family": "registry",
+ "target": "pottsmpnn",
+ "weights": "random",
+ "rule": "encoder h_V after 3 layers, masked mean",
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+ "weights_sha256": "fd9636d73a1e9994",
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+}

probing_embeddings/prostt5/meta.json

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+{
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+ "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",
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+ "n_layers": 24,
+ "n_parameters": 1208164352,
+ "inputs_passed": "amino-acid sequence only",
+ "dataset": "protcompass/probing_data/labels.h5",
+ "date": "2026-09-19 19:53",
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+}

probing_embeddings/tfn/meta.json

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+{
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+ "target": "tfn",
+ "weights": "random",
+ "rule": "final invariant node states of the wrapper, masked mean over valid residues",
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+ "weights_sha256": "b07ce6d9887ef8db",
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