diff --git a/confirmation/embeddings/ankh_base/meta.json b/confirmation/embeddings/ankh_base/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..c247403ab0e2339b3e38a698fbf0ff64a4408bb5 --- /dev/null +++ b/confirmation/embeddings/ankh_base/meta.json @@ -0,0 +1,37 @@ +{ + "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", + "dataset": "protcompass/confirmation/labels_v44.h5", + "date": "2026-09-22 16:03", + "seconds": 20.3, + "n_domains": 1990, + "dim": 768, + "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5", + "health": 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0000000000000000000000000000000000000000..224f3eecb09f520bc73c6258a0e1fb106ee3726a --- /dev/null +++ b/confirmation2/embeddings/prottrans_t5_xl_u50/meta.json @@ -0,0 +1,37 @@ +{ + "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", + "dataset": "protcompass/confirmation2/labels_v44.h5", + "date": "2026-09-23 14:00", + "seconds": 35.2, + "n_domains": 1316, + "dim": 1024, + "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5", + "health": { + "n_rows": 1316, + "dim": 1024, + "nan_values": 0, + "all_zero_rows": 0, 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residue embeddings, sequence track only; structure track masked, no coordinates", + "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: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "ec_classification", + "date": "2026-09-25 15:58", + "seconds": 742.0, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/ec_classification.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, + 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"pretrained", + "rule": "final hidden states at the L residue positions of AA+3Di tokens, 3Di string permuted within the protein (seed from sha256 of the protein id)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "ec_classification", + "date": "2026-09-25 16:01", + "seconds": 980.0, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/ec_classification.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 3000, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10500, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10500, + "numerical_rank": 1279, + "max_abs": 1.4703494310379028 + }, + "input_audit": { + "rel_change_jitter_1A": 0.43988864170452435, + "rel_change_coord_swap": 0.322458235413735, + "rel_change_seq_shuffle": 0.24153720608178586, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/go_bp/esm3_seqonly/ids_test.txt b/extract/ab_modality/embeddings/go_bp/esm3_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..251e9419b51fb51d5c3c81d29efbffc6128e3efb --- /dev/null +++ b/extract/ab_modality/embeddings/go_bp/esm3_seqonly/ids_test.txt @@ -0,0 +1,2903 @@ +11as_A +2fvl_A +5kdw_A +2fv8_A +5keg_A +2fsi_A +5kjs_A +2fwm_X +2fq1_A +5kpt_A +5kpw_E +5kq4_D +2fj9_A +2fhg_A +2fge_A +2fp2_A +5kcv_A +5kbw_A +2fyo_A +2gf0_A +2gdz_A +2gbg_A +5jzv_A +2gae_A +2g9b_A +5k22_A +5k23_A 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track: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "go_bp", + "date": "2026-09-25 15:46", + "seconds": 642.4, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_bp.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": 2903, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10403, + "dim": 1536, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10384, + "numerical_rank": 1536, + "max_abs": 12387.6025390625 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.27526844623722635, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} diff --git a/extract/ab_modality/embeddings/go_bp/saprot_seqonly/ids_test.txt b/extract/ab_modality/embeddings/go_bp/saprot_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..251e9419b51fb51d5c3c81d29efbffc6128e3efb --- /dev/null +++ b/extract/ab_modality/embeddings/go_bp/saprot_seqonly/ids_test.txt @@ -0,0 +1,2903 @@ +11as_A +2fvl_A +5kdw_A +2fv8_A +5keg_A +2fsi_A +5kjs_A +2fwm_X +2fq1_A +5kpt_A +5kpw_E +5kq4_D +2fj9_A +2fhg_A +2fge_A +2fp2_A +5kcv_A +5kbw_A +2fyo_A +2gf0_A +2gdz_A +2gbg_A +5jzv_A +2gae_A +2g9b_A +5k22_A +5k23_A +2g5w_A +2g3t_A +2g2o_A +2g2b_A +5k98_A +5kar_A +5kb6_A +5kuf_A +2gf5_A +2fem_A +2fbq_A +5l8w_A +5la7_A +2exx_A +2exu_A +2ex6_A +2ewn_A +2f11_A +5lbt_A +2evl_A +2et1_A +2esb_A +5ld2_D +2erv_A +2el9_A +2ew1_A +5l8o_A +2f2p_A +5l7m_A +5kzw_A +5l0v_A +5l13_A +2f9y_B +2f9l_A +2f9j_A +2f9g_A +2f8a_A +5l3d_A +2f7s_A +2f7k_A +2f73_A +5l46_A +5l4k_V +5l6w_C +5kwy_C +5lef_A +5jwy_A +2gia_B +2hw5_A +2hw4_A +2hw1_A 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/dev/null +++ b/extract/ab_modality/embeddings/go_bp/saprot_seqonly/meta.json @@ -0,0 +1,41 @@ +{ + "encoder": "saprot_seqonly", + "family": "patched", + "target": "saprot_seqonly", + "weights": "pretrained", + "rule": "final hidden states at the L residue positions of AA+'#' tokens (3Di masked)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: '#' (masked structure token) at every residue", + "patch": "patched/saprot_seqonly.py (modality ablation of patched/saprot_hf.py)", + "task": "go_bp", + "date": "2026-09-25 15:53", + "seconds": 894.8, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_bp.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": 2903, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10403, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10384, + "numerical_rank": 1279, + "max_abs": 2.2824113368988037 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.3560794577750009, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/go_bp/saprot_shuf3di/ids_test.txt b/extract/ab_modality/embeddings/go_bp/saprot_shuf3di/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..251e9419b51fb51d5c3c81d29efbffc6128e3efb --- /dev/null +++ b/extract/ab_modality/embeddings/go_bp/saprot_shuf3di/ids_test.txt @@ -0,0 +1,2903 @@ +11as_A +2fvl_A +5kdw_A +2fv8_A +5keg_A +2fsi_A +5kjs_A +2fwm_X +2fq1_A +5kpt_A +5kpw_E +5kq4_D +2fj9_A +2fhg_A +2fge_A +2fp2_A +5kcv_A +5kbw_A +2fyo_A +2gf0_A +2gdz_A +2gbg_A +5jzv_A +2gae_A 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"n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "go_bp", + "date": "2026-09-25 16:34", + "seconds": 983.7, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_bp.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": 2903, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10403, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10403, + "numerical_rank": 1279, + "max_abs": 1.4106837511062622 + }, + "input_audit": { + "rel_change_jitter_1A": 0.43988864170452435, + "rel_change_coord_swap": 0.322458235413735, + "rel_change_seq_shuffle": 0.24153720608178586, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/go_mf/esm3_seqonly/ids_test.txt b/extract/ab_modality/embeddings/go_mf/esm3_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..85ab7b30fd8f1dbf720717964109e124fbea064e --- /dev/null +++ b/extract/ab_modality/embeddings/go_mf/esm3_seqonly/ids_test.txt @@ -0,0 +1,2904 @@ +11as_A +2riu_A +1ocu_A +6aag_A +4zrp_A +4ztt_A +4zwb_A +4zwn_A +2rdu_A +1ogp_A +6a66_A +2rd2_A +2rkb_A +2rcq_A +6a5q_B +1oi2_A +6a5l_b +2rcm_A +4zyn_A +1oip_A +4zzl_A +1oj6_A +2ra4_A +6a4i_A +2r92_I +1ohw_A +1okg_A +2rkn_A +4znq_A +6ah3_G +1o5w_A +6ah3_E +6ah3_B +6ah0_t +2ucz_A +2tmk_A +4zgx_A +4zgz_A +4zi3_A +4zir_B +2rkq_A +6agb_K +1o8b_A +6agb_F +1o8t_A +1o92_A +6agb_D +6agb_C +2rsv_A +4zk0_A +4zlt_F +2rnb_A +1oat_A +6agb_I +2r8p_A +5a2o_A +5a2q_T +2qxl_A +5ac2_A +5aex_A +2qty_A +2qtv_A +2qt9_A +5afi_h +5zrv_A +2qry_A +2qrw_A 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b/extract/ab_modality/embeddings/go_mf/esm3_seqonly/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..621c7fd73ff2773f122cd71cef9480b1fd88d1a3 --- /dev/null +++ b/extract/ab_modality/embeddings/go_mf/esm3_seqonly/meta.json @@ -0,0 +1,41 @@ +{ + "encoder": "esm3_seqonly", + "family": "patched", + "target": "esm3_seqonly", + "weights": "pretrained", + "rule": "final trunk residue embeddings, sequence track only; structure track masked, no coordinates", + "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: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "go_mf", + "date": "2026-09-25 15:35", + "seconds": 543.4, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_mf.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 2904, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10404, + "dim": 1536, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10385, + "numerical_rank": 1536, + "max_abs": 13089.6845703125 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.27526844623722635, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} diff --git a/extract/ab_modality/embeddings/go_mf/saprot_seqonly/ids_test.txt b/extract/ab_modality/embeddings/go_mf/saprot_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..85ab7b30fd8f1dbf720717964109e124fbea064e --- /dev/null +++ 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of AA+'#' tokens (3Di masked)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: '#' (masked structure token) at every residue", + "patch": "patched/saprot_seqonly.py (modality ablation of patched/saprot_hf.py)", + "task": "go_mf", + "date": "2026-09-25 15:38", + "seconds": 704.1, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_mf.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 2904, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10404, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10385, + "numerical_rank": 1279, + "max_abs": 2.20894455909729 + }, + "input_audit": { + "rel_change_jitter_1A": 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+5uve_A +1lrw_B diff --git a/extract/ab_modality/embeddings/go_mf/saprot_shuf3di/meta.json b/extract/ab_modality/embeddings/go_mf/saprot_shuf3di/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..97f273368adcd48ab717a774d04b232f08c4ed74 --- /dev/null +++ b/extract/ab_modality/embeddings/go_mf/saprot_shuf3di/meta.json @@ -0,0 +1,41 @@ +{ + "encoder": "saprot_shuf3di", + "family": "patched", + "target": "saprot_shuf3di", + "weights": "pretrained", + "rule": "final hidden states at the L residue positions of AA+3Di tokens, 3Di string permuted within the protein (seed from sha256 of the protein id)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "go_mf", + "date": "2026-09-25 16:17", + "seconds": 965.4, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/go_mf.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 2904, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10404, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10404, + "numerical_rank": 1279, + "max_abs": 1.4106837511062622 + }, + "input_audit": { + "rel_change_jitter_1A": 0.43988864170452435, + "rel_change_coord_swap": 0.322458235413735, + "rel_change_seq_shuffle": 0.24153720608178586, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/membrane_soluble/esm3_seqonly/ids_test.txt 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0000000000000000000000000000000000000000..0e0bce491c0627f3cf9fb3db1ec79d04c622ee9a --- /dev/null +++ b/extract/ab_modality/embeddings/membrane_soluble/esm3_seqonly/meta.json @@ -0,0 +1,41 @@ +{ + "encoder": "esm3_seqonly", + "family": "patched", + "target": "esm3_seqonly", + "weights": "pretrained", + "rule": "final trunk residue embeddings, sequence track only; structure track masked, no coordinates", + "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: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "membrane_soluble", + "date": "2026-09-25 16:40", + "seconds": 948.9, + "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": 11535.349609375 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.27526844623722635, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} diff --git a/extract/ab_modality/embeddings/membrane_soluble/saprot_seqonly/ids_test.txt b/extract/ab_modality/embeddings/membrane_soluble/saprot_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113 --- /dev/null +++ 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+ "encoder": "saprot_seqonly", + "family": "patched", + "target": "saprot_seqonly", + "weights": "pretrained", + "rule": "final hidden states at the L residue positions of AA+'#' tokens (3Di masked)", + "env": "protein_embeddings", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: '#' (masked structure token) at every residue", + "patch": "patched/saprot_seqonly.py (modality ablation of patched/saprot_hf.py)", + "task": "membrane_soluble", + "date": "2026-09-25 16:29", + "seconds": 854.8, + "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": 2.2932915687561035 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.3560793634995905, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_test.txt b/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..026c643368aa746c80ee9a2896e32c734796e113 --- /dev/null +++ b/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_test.txt @@ -0,0 +1,3000 @@ +Q28165 +O14236 +Q6AXV4 +P32037 +Q9S736 +Q9LUB7 +Q9UT93 +P02655 +P11169 +O95865 +Q9XGZ0 +Q9Y7Y7 +P40345 +Q3UMZ3 +Q9JIF5 +Q9HBB8 +Q9LYG3 +Q9HCN2 +O23144 +Q8J0D5 +Q8NIH1 +Q70Z53 +Q15036 +Q59UT5 +D0NRP3 +Q6PEC3 +I7GQA7 +Q9QYR7 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a/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_train.txt b/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_train.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f486f2bbbacad80d6657598f47637f9d0c60c0e --- /dev/null +++ b/extract/ab_modality/embeddings/membrane_soluble/saprot_shuf3di/ids_train.txt @@ -0,0 +1,6000 @@ +Q9D6Y1 +Q9H6X4 +Q9XFR0 +P22646 +P62022 +O14804 +P90920 +Q9VYM3 +Q9FXA8 +Q9P7Z6 +Q8MVA6 +O43924 +Q9LFU9 +Q9S823 +Q8WUU5 +P39714 +Q95142 +P0C0W9 +Q14BK3 +O55057 +Q68CJ6 +O57385 +O94598 +Q8BRK8 +Q6SKR5 +Q9VWU1 +Q9ERR2 +Q57YZ9 +Q5TKA1 +O43405 +P29218 +O64948 +Q03557 +Q9Y7R1 +O00299 +O74168 +Q8VYF9 +Q23243 +P02748 +Q64536 +Q8WZJ4 +Q570C0 +P11441 +Q09683 +O60664 +Q8NFX7 +Q06817 +Q1T763 +P00749 +Q3E785 +Q86UT6 +Q13084 +Q12010 +Q8R4Z9 +P49590 +Q9NQE9 +O60237 +P83774 +Q711A6 +P48740 +P0DH95 +A8PZM4 +O42890 +Q9BRF8 +Q9H0N0 +Q9LY23 +O00399 +P51957 +P33441 +O54714 +P97478 +Q5A6U1 +Q13886 +Q8ITC9 +Q9T074 +Q92558 +Q9NQ48 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tokens, 3Di string permuted within the protein (seed from sha256 of the protein id)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "membrane_soluble", + "date": "2026-09-25 16:40", + "seconds": 1223.4, + "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": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10500, + "numerical_rank": 1279, + "max_abs": 2.178069591522217 + }, + "input_audit": { + "rel_change_jitter_1A": 0.43988864170452435, + "rel_change_coord_swap": 0.322458235413735, + "rel_change_seq_shuffle": 0.24153720608178586, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/ppi_affinity/esm3_seqonly/ids_chains.txt b/extract/ab_modality/embeddings/ppi_affinity/esm3_seqonly/ids_chains.txt new file mode 100644 index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0 --- /dev/null +++ b/extract/ab_modality/embeddings/ppi_affinity/esm3_seqonly/ids_chains.txt @@ -0,0 +1,2589 @@ +chain_c605c8c1d8bd +chain_7ecce6a26a63 +chain_51aa55454639 +chain_40047354f1c4 +chain_53b53a21d59a +chain_18e8da160412 +chain_e496b708eac5 +chain_33b883bd38c8 +chain_c05205b8e790 +chain_58d194be0d80 +chain_631549834118 +chain_7a36690be49f +chain_dff75d440bf3 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"rule": "final trunk residue embeddings, sequence track only; structure track masked, no coordinates", + "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: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "ppi_affinity", + "date": "2026-09-25 15:08", + "seconds": 98.9, + "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": 1536, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 2589, + "numerical_rank": 1536, + "max_abs": 10995.62890625 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.27526844623722635, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} diff --git a/extract/ab_modality/embeddings/ppi_affinity/saprot_seqonly/ids_chains.txt b/extract/ab_modality/embeddings/ppi_affinity/saprot_seqonly/ids_chains.txt new file mode 100644 index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0 --- /dev/null +++ b/extract/ab_modality/embeddings/ppi_affinity/saprot_seqonly/ids_chains.txt @@ -0,0 +1,2589 @@ +chain_c605c8c1d8bd +chain_7ecce6a26a63 +chain_51aa55454639 +chain_40047354f1c4 +chain_53b53a21d59a +chain_18e8da160412 +chain_e496b708eac5 +chain_33b883bd38c8 +chain_c05205b8e790 +chain_58d194be0d80 +chain_631549834118 +chain_7a36690be49f +chain_dff75d440bf3 +chain_b3cd77c126fe +chain_574772c53458 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L residue positions of AA+'#' tokens (3Di masked)", + "env": "base", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: '#' (masked structure token) at every residue", + "patch": "patched/saprot_seqonly.py (modality ablation of patched/saprot_hf.py)", + "task": "ppi_affinity", + "date": "2026-09-25 15:08", + "seconds": 100.4, + "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": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 2589, + "numerical_rank": 1279, + "max_abs": 2.2027549743652344 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.3560794577750009, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/ppi_affinity/saprot_shuf3di/ids_chains.txt b/extract/ab_modality/embeddings/ppi_affinity/saprot_shuf3di/ids_chains.txt new file mode 100644 index 0000000000000000000000000000000000000000..8476d4f0eae0217f3eb51c65d62a136e31f0adf0 --- /dev/null +++ b/extract/ab_modality/embeddings/ppi_affinity/saprot_shuf3di/ids_chains.txt @@ -0,0 +1,2589 @@ +chain_c605c8c1d8bd +chain_7ecce6a26a63 +chain_51aa55454639 +chain_40047354f1c4 +chain_53b53a21d59a +chain_18e8da160412 +chain_e496b708eac5 +chain_33b883bd38c8 +chain_c05205b8e790 +chain_58d194be0d80 +chain_631549834118 +chain_7a36690be49f +chain_dff75d440bf3 +chain_b3cd77c126fe +chain_574772c53458 +chain_2e8b291dd2d2 +chain_2d1ac440b7f4 +chain_877e1bae429d +chain_a91f01cae823 +chain_b310cc32aa6d 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the protein id)", + "env": "protein_embeddings", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "ppi_affinity", + "date": "2026-09-25 16:19", + "seconds": 219.4, + "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": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 2589, + "numerical_rank": 1279, + "max_abs": 1.4178855419158936 + }, + "input_audit": { + "rel_change_jitter_1A": 0.4398886288765328, + "rel_change_coord_swap": 0.32245820448696383, + "rel_change_seq_shuffle": 0.2415372871701812, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/remote_homology/esm3_seqonly/ids_test.txt b/extract/ab_modality/embeddings/remote_homology/esm3_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4 --- /dev/null +++ b/extract/ab_modality/embeddings/remote_homology/esm3_seqonly/ids_test.txt @@ -0,0 +1,480 @@ +d1twfl_ +d1b3qa2 +d2p5zx1 +d1k28a1 +d1j6qa_ +d3d3ra1 +d2ot2a1 +d2z1ca1 +d2k5wa1 +d2k5qa1 +d1n4ka2 +d1mrza1 +d1n08a_ +d2oq0a2 +d1nb9a_ +d1vloa1 +d1vlya1 +d1wosa1 +d1v5va1 +d2jdid2 +d1skyb2 +d1skye2 +d1mabb2 +d1fx0a2 +d2jdia2 +d1vhea1 +d1yloa1 +d3ctaa2 +d2grea1 +d2oq0a1 +d2qi2a1 +d2c34a1 +d1xzwa1 +d1o75a2 +d1o75a1 +d2cu9a1 +d1k5ja_ +d1nlqa_ +d1stma_ +d1p2za1 +d1m3ya1 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"esm3-sm-open-v1/data/weights/esm3_sm_open_v1.pth", + "dtype": "bfloat16", + "n_parameters": 1401735748, + "inputs_passed": "sequence track: true residues; structure track: mask token at every position (no coordinates, so no VQ-VAE tokens and no geometric attention input); function, SASA and secondary-structure tracks at their defaults", + "patch": "patched/esm3_seqonly.py (modality ablation of patched/esm3_inproc.py)", + "task": "remote_homology", + "date": "2026-09-25 15:13", + "seconds": 283.4, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/remote_homology.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 480, + "train": 6000, + "valid": 506 + }, + "health": { + "n_rows": 6986, + "dim": 1536, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 6985, + "numerical_rank": 1536, + "max_abs": 12815.421875 + }, 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"d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: '#' (masked structure token) at every residue", + "patch": "patched/saprot_seqonly.py (modality ablation of patched/saprot_hf.py)", + "task": "remote_homology", + "date": "2026-09-25 15:14", + "seconds": 316.0, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/remote_homology.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 480, + "train": 6000, + "valid": 506 + }, + "health": { + "n_rows": 6986, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 6985, + "numerical_rank": 1279, + "max_abs": 2.2533810138702393 + }, + "input_audit": { + "rel_change_jitter_1A": 0.0, + "rel_change_coord_swap": 0.0, + "rel_change_seq_shuffle": 0.3560794577750009, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/remote_homology/saprot_shuf3di/ids_test.txt b/extract/ab_modality/embeddings/remote_homology/saprot_shuf3di/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..c46b3a1696b9fce415e50d4700af7aabae77b2c4 --- /dev/null +++ b/extract/ab_modality/embeddings/remote_homology/saprot_shuf3di/ids_test.txt @@ -0,0 +1,480 @@ +d1twfl_ +d1b3qa2 +d2p5zx1 +d1k28a1 +d1j6qa_ +d3d3ra1 +d2ot2a1 +d2z1ca1 +d2k5wa1 +d2k5qa1 +d1n4ka2 +d1mrza1 +d1n08a_ +d2oq0a2 +d1nb9a_ +d1vloa1 +d1vlya1 +d1wosa1 +d1v5va1 +d2jdid2 +d1skyb2 +d1skye2 +d1mabb2 +d1fx0a2 +d2jdia2 +d1vhea1 +d1yloa1 +d3ctaa2 +d2grea1 +d2oq0a1 +d2qi2a1 +d2c34a1 +d1xzwa1 +d1o75a2 +d1o75a1 +d2cu9a1 +d1k5ja_ +d1nlqa_ +d1stma_ +d1p2za1 +d1m3ya1 +d1m3ya2 +d1hx6a1 +d2vgna1 +d1hx6a2 +d2pr9a1 +d1f0la1 +d1h8la1 +d2oqea1 +d1w2za1 +d1hyoa1 +d2heqa1 +d2dk3a1 +d2eyqa1 +d1y71a1 +d1auua_ +d1ib8a1 +d2d9ra1 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"n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "remote_homology", + "date": "2026-09-25 15:45", + "seconds": 508.7, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/remote_homology.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 480, + "train": 6000, + "valid": 506 + }, + "health": { + "n_rows": 6986, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 6986, + "numerical_rank": 1279, + "max_abs": 1.3415688276290894 + }, + "input_audit": { + "rel_change_jitter_1A": 0.43988864170452435, + "rel_change_coord_swap": 0.322458235413735, + "rel_change_seq_shuffle": 0.24153720608178586, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/stability/esm3_seqonly/ids_test.txt b/extract/ab_modality/embeddings/stability/esm3_seqonly/ids_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..e8ca8a6b32e54aa2656f3351ad493d8975116e5e --- /dev/null +++ b/extract/ab_modality/embeddings/stability/esm3_seqonly/ids_test.txt @@ -0,0 +1,3000 @@ +EEHEE_rd3_0037.pdb_A19G__test_000004 +EEHEE_rd3_0037.pdb_A19H__test_000005 +EEHEE_rd3_0037.pdb_A19I__test_000006 +EEHEE_rd3_0037.pdb_A19S__test_000014 +EEHEE_rd3_0037.pdb_A19T__test_000015 +EEHEE_rd3_0037.pdb_A19Y__test_000018 +EEHEE_rd3_0037.pdb_A20D__test_000019 +EEHEE_rd3_0037.pdb_A20G__test_000022 +EEHEE_rd3_0037.pdb_A20H__test_000023 +EEHEE_rd3_0037.pdb_A20M__test_000027 +EEHEE_rd3_0037.pdb_A20V__test_000034 +EEHEE_rd3_0037.pdb_A22G__test_000040 +EEHEE_rd3_0037.pdb_A22I__test_000042 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a/extract/ab_modality/embeddings/stability/saprot_shuf3di/meta.json b/extract/ab_modality/embeddings/stability/saprot_shuf3di/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..58cac60bc676fd5db4c31905f65fcb79c8337952 --- /dev/null +++ b/extract/ab_modality/embeddings/stability/saprot_shuf3di/meta.json @@ -0,0 +1,41 @@ +{ + "encoder": "saprot_shuf3di", + "family": "patched", + "target": "saprot_shuf3di", + "weights": "pretrained", + "rule": "final hidden states at the L residue positions of AA+3Di tokens, 3Di string permuted within the protein (seed from sha256 of the protein id)", + "env": "protein_embeddings", + "checkpoint": "westlake-repl/SaProt_650M_AF2", + "checkpoint_revision": "d9b9ad00ef61c0990e611b2b43f2231c7de24b38", + "n_parameters": 651242901, + "inputs_passed": "amino-acid track: real sequence; 3Di track: real mini3di tokens permuted within the protein (seed = first 8 bytes of sha256(protein id)); no pLDDT masking", + "patch": "patched/saprot_shuf3di.py (control for patched/saprot_seqonly.py)", + "task": "stability", + "date": "2026-09-25 16:25", + "seconds": 604.6, + "pooling": "masked mean over all residues of the chain", + "manifest": "manifest/stability.csv", + "rows": "stage1 == 1", + "structure_coverage": "every row has a structure file whose sequence equals the task sequence (see manifest/coverage.csv)", + "n_per_split": { + "test": 3000, + "train": 6000, + "valid": 1500 + }, + "health": { + "n_rows": 10500, + "dim": 1280, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 10500, + "numerical_rank": 1279, + "max_abs": 1.7159743309020996 + }, + "input_audit": { + "rel_change_jitter_1A": 0.4398886288765328, + "rel_change_coord_swap": 0.32245820448696383, + "rel_change_seq_shuffle": 0.2415372871701812, + "rel_change_rigid_motion": 0.0, + "verdict": "pass" + } +} \ No newline at end of file diff --git a/extract/ab_modality/embeddings/subcellular_localization/saprot_seqonly/ids_test.txt 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"official architecture, random weights; 100 scalar channels + 16 vector norms per residue", + "weights": "random", + "seed": null, + "checkpoint": null, + "checkpoint_sha256": null, + "weights_sha256": "cdec9adf86f7cd39", + "weights_sha256_released": "cdec9adf86f7cd39", + "frame_coordinates": "N, CA, C atoms of the structure file as passed to GCPNet", + "env": "gcpnet", + "script": "protcompass/extract/extract_vector_frame.py", + "dataset": "protcompass/probing_data/labels.h5", + "date": "2026-09-23 23:11", + "seconds_extraction": 3238.9, + "seconds_total": 3249.4, + "n_domains": 19461, + "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5; pooled_fp32.npy row k is protein k (mean over its residues)", + "health": { + "n_rows": 19461, + "dim": 148, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 19461, + "numerical_rank": 148, + "max_abs": 2.1440465450286865 + }, + "verification_vs_released": { + "a_scalar_maxabs_fp16_vs_released": 0.001953125, + "a_scalar_n_mismatch": 288907, + "a_scalar_max_diff_in_fp16_ulps": 11.0, + "a_released_rule_maxabs_vs_released": 0.001953125, + "b_norm_maxabs_fp32_vs_released": 0.0004887580871582031, + "b_norm_maxabs_fp16stored_vs_released": 0.0009765625, + "b_norm_maxrel_fp32_vs_released": 0.0004834467821782178, + "b_norm_max_diff_fp16stored_in_fp16_ulps": 1.0, + "b_projection_norm_maxabs_vs_unprojected": 2.5040619444638423e-07, + "n_values_scalar": 282352500, + "n_values_norm": 45176400, + "a_pooled_scalar_maxabs_vs_released": 7.152557373046875e-07 + }, + "rigid_motion_invariance": { + "median_rel_change_new": 5.07799771188054e-08, + "median_rel_change_released_rule": 2.0047920024269614e-08, + "median_rel_change_atommean": 2.55413858534988e-08, + "max_rel_change_new": 1.9257635560836783e-05, + "max_rel_change_released_rule": 2.0232596446077114e-05, + "max_rel_change_atommean": 2.567175203075254e-05, + "n_proteins": 32, + "motion": "random proper rotation (QR of a Gaussian matrix) and a Gaussian translation of scale 10 A, applied to the input coordinates (GVP, MACE) or to every atom of the structure (GCPNet)", + "proteins": "the 32 proteins of the released input audit (input_audit.audit_proteins('probing'))" + }, + "extra_files": { + "residue_atommean_fp16.npy": "[mean_a h_a (100), mean_a F_i @ chi_a (48)] per residue, a = heavy atoms of residue i", + "pooled_atommean_fp32.npy": "mean over residues of residue_atommean_fp16.npy (from fp32)" + }, + "health_atommean": { + "n_rows": 19461, + "dim": 148, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 19461, + "numerical_rank": 147, + "max_abs": 2.1440465450286865 + } +} diff --git a/probing_embeddings_vframe/mace_vframe/meta.json b/probing_embeddings_vframe/mace_vframe/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..aae5c2e7f16832a01fdb94cf54aa80c1f30aa7dd --- /dev/null +++ b/probing_embeddings_vframe/mace_vframe/meta.json @@ -0,0 +1,61 @@ +{ + "encoder": "mace_vframe", + "source_encoder": "mace", + "source_dir": "protcompass/probing_embeddings/mace", + "representation": "[scalar channels (s), frame-projected vector channels (3v)]", + "s": 128, + "v": 16, + "dim": 176, + "frame": "F_i rows (x, y, z): x = (C - CA)/|C - CA|, z = x cross (N - CA) normalised, y = z cross x (protcompass/scripts/prereg_floors.py frame); vector block = F_i @ v_c(i) for c = 1..v, channel-major (v1x, v1y, v1z, v2x, ...)", + "vector_source": "vector channels v (16 x 3) of the last MACEBlock output, captured by a forward hook; the released wrapper output (output_proj of the scalars, 128) does not contain them in any form", + "scalar_source": "the released scalar columns, recomputed in the same forward pass", + "released_rule": "final invariant node states of the wrapper, masked mean over valid residues", + "weights": "random", + "seed": 20260919, + "checkpoint": null, + "checkpoint_sha256": null, + "weights_sha256": "e8e9d6fd9722cc4e", + "weights_sha256_released": "e8e9d6fd9722cc4e", + "frame_coordinates": "N, CA, C of the coordinates passed to the model (labels.h5 coords centred on the CA centroid, as released)", + "env": "protein_embeddings", + "script": "protcompass/extract/extract_vector_frame.py", + "dataset": "protcompass/probing_data/labels.h5", + "date": "2026-09-23 22:37", + "seconds_extraction": 754.3, + "seconds_total": 759.5, + "n_domains": 19461, + "row_convention": "row r of residue_fp16.npy is row r of residue/* in labels.h5; pooled_fp32.npy row k is protein k (mean over its residues)", + "health": { + "n_rows": 19461, + "dim": 176, + "nan_values": 0, + "all_zero_rows": 0, + "distinct_rows": 19461, + "numerical_rank": 175, + "max_abs": 1.3848251104354858 + }, + "verification_vs_released": { + "a_scalar_maxabs_fp16_vs_released": 0.0, + "a_scalar_n_mismatch": 0, + "a_scalar_max_diff_in_fp16_ulps": 0.0, + "a_released_rule_maxabs_vs_released": 0.0, + "b_norm_maxabs_fp32_vs_released": null, + "b_norm_maxabs_fp16stored_vs_released": null, + "b_norm_maxrel_fp32_vs_released": null, + "b_norm_max_diff_fp16stored_in_fp16_ulps": null, + "b_projection_norm_maxabs_vs_unprojected": 6.972807513605517e-07, + "n_values_scalar": 361411200, + "n_values_norm": 0, + "a_pooled_scalar_maxabs_vs_released": 0.0, + "b_note": "not applicable: the released MACE embedding (output_proj of the 128 scalar channels) contains no vector columns, neither norms nor components; b_projection_norm_maxabs_vs_unprojected checks that the projection preserves each channel's norm" + }, + "rigid_motion_invariance": { + "median_rel_change_new": 1.5030455055432288e-07, + "median_rel_change_released_rule": 4.749255819363497e-08, + "max_rel_change_new": 9.565903171161352e-07, + "max_rel_change_released_rule": 6.331365051121389e-08, + "n_proteins": 32, + "motion": "random proper rotation (QR of a Gaussian matrix) and a Gaussian translation of scale 10 A, applied to the input coordinates (GVP, MACE) or to every atom of the structure (GCPNet)", + "proteins": "the 32 proteins of the released input audit (input_audit.audit_proteins('probing'))" + } +}