Upload five finalized 20M ligand shards
Browse files- .gitattributes +5 -0
- shard_1/metadata.json +68 -0
- shard_1/train.lmdb +3 -0
- shard_2/metadata.json +61 -0
- shard_2/train.lmdb +3 -0
- shard_3/metadata.json +66 -0
- shard_3/train.lmdb +3 -0
- shard_4/metadata.json +79 -0
- shard_4/train.lmdb +3 -0
- shard_5/metadata.json +79 -0
- shard_5/train.lmdb +3 -0
.gitattributes
CHANGED
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@@ -58,3 +58,8 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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shard_1/train.lmdb filter=lfs diff=lfs merge=lfs -text
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shard_2/train.lmdb filter=lfs diff=lfs merge=lfs -text
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shard_3/train.lmdb filter=lfs diff=lfs merge=lfs -text
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shard_4/train.lmdb filter=lfs diff=lfs merge=lfs -text
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shard_5/train.lmdb filter=lfs diff=lfs merge=lfs -text
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shard_1/metadata.json
ADDED
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@@ -0,0 +1,68 @@
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{
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"base_registry_unique": 19999982,
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"base_seen_lmdb": "/scratch/shai/data_20m_selfies_original_cartesian_shards/selfies_seen.lmdb",
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| 4 |
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"conformers_per_molecule": 10,
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| 5 |
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"coordinate_contract": "coordinates[:, i, :] matches atom i after SELFIES decode and RDKit parse",
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"coordinate_space": "original RDKit Cartesian coordinates; atom-axis permutation only",
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| 7 |
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"discarded_after_split_filled": 0,
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| 8 |
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"duplicate_selfies_in_base_rejected": 6,
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| 9 |
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"duplicate_selfies_in_shard_rejected": 9158,
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"elapsed_seconds": 8426.422278642654,
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"finished_at_epoch": 1787190989.081326,
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"local_registry_digest_entries": 20000000,
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| 13 |
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"local_registry_extra_entries_from_resume": 0,
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| 14 |
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"local_registry_unique": 20000000,
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"molecular_property_contract": {
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"calculated_from": "canonical heavy-atom molecule represented by smi; standard implicit hydrogens are included by RDKit",
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"molecular_weight_kind": "average molecular weight, not exact isotope mass",
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"rdkit_version": "2025.03.6",
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"sa_score_implementation": "RDKit Contrib SA_Score/sascorer.py"
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},
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"partition_count": 5,
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"partition_index": 0,
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"partition_rejected": 6796319,
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"raw_slices": [
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1,
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2,
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3,
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4,
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5
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],
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"record_format": {
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"atoms": "heavy-atom symbols in decoded SELFIES atom order",
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"coordinates": "float32 ndarray, shape (10, n_heavy, 3)",
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"mol_log_p": "float; RDKit Crippen.MolLogP",
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"molecular_weight": "float; RDKit Descriptors.MolWt",
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"qed": "float; RDKit QED.qed",
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"sa_score": "float; RDKit Contrib SA_Score; 1 is easiest and 10 is hardest",
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"smi": "SELFIES encoding of canonical isomeric heavy-atom SMILES",
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"tpsa": "float; RDKit rdMolDescriptors.CalcTPSA"
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},
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"resume": {
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"enabled": true,
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"resumed_from_train": 18309263,
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"resumed_from_val": 0,
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"source_records_skipped": 91564160
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},
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"skipped_by_reason": {
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"coordinates_shape": 6638
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},
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"source_file_error_samples": [],
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"source_file_errors": {},
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"source_processed": {
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"raw_zinc": 8502912
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},
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"source_written": {
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"raw_zinc": 1690737
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},
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"split": "all accepted records assigned to train",
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| 59 |
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"started_at_epoch": 1787182562.6590474,
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| 60 |
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"total_examples": 20000000,
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| 61 |
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"train_examples": 20000000,
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| 62 |
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"val_examples": 0,
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| 63 |
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"validation": {
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| 64 |
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"selfies_roundtrip_every": 10000,
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| 65 |
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"smoke_test": false
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| 66 |
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},
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"workers": 192
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}
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shard_1/train.lmdb
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:499368580f8dacc2fb844b867c8c1695f5d5a4aaffa2314122fea04191b49e9a
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size 86753845248
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shard_2/metadata.json
ADDED
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@@ -0,0 +1,61 @@
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{
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| 2 |
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"base_registry_unique": 19999982,
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| 3 |
+
"base_seen_lmdb": "/scratch/shai/data_20m_selfies_original_cartesian_shards/selfies_seen.lmdb",
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| 4 |
+
"conformers_per_molecule": 10,
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| 5 |
+
"coordinate_contract": "coordinates[:, i, :] matches atom i after SELFIES decode and RDKit parse",
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| 6 |
+
"coordinate_space": "original RDKit Cartesian coordinates; atom-axis permutation only",
|
| 7 |
+
"discarded_after_split_filled": 0,
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| 8 |
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"duplicate_selfies_in_base_rejected": 23,
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| 9 |
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"duplicate_selfies_in_shard_rejected": 68,
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| 10 |
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"elapsed_seconds": 84522.61968636513,
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| 11 |
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"finished_at_epoch": 1787110423.9621181,
|
| 12 |
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"local_registry_unique": 20000000,
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| 13 |
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"molecular_property_contract": {
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| 14 |
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"calculated_from": "canonical heavy-atom molecule represented by smi; standard implicit hydrogens are included by RDKit",
|
| 15 |
+
"molecular_weight_kind": "average molecular weight, not exact isotope mass",
|
| 16 |
+
"rdkit_version": "2025.03.6",
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| 17 |
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"sa_score_implementation": "RDKit Contrib SA_Score/sascorer.py"
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| 18 |
+
},
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| 19 |
+
"partition_count": 5,
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| 20 |
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"partition_index": 1,
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| 21 |
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"partition_rejected": 79990241,
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| 22 |
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"raw_slices": [
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2,
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3,
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4,
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5,
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1
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],
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| 29 |
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"record_format": {
|
| 30 |
+
"atoms": "heavy-atom symbols in decoded SELFIES atom order",
|
| 31 |
+
"coordinates": "float32 ndarray, shape (10, n_heavy, 3)",
|
| 32 |
+
"mol_log_p": "float; RDKit Crippen.MolLogP",
|
| 33 |
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"molecular_weight": "float; RDKit Descriptors.MolWt",
|
| 34 |
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"qed": "float; RDKit QED.qed",
|
| 35 |
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"sa_score": "float; RDKit Contrib SA_Score; 1 is easiest and 10 is hardest",
|
| 36 |
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"smi": "SELFIES encoding of canonical isomeric heavy-atom SMILES",
|
| 37 |
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"tpsa": "float; RDKit rdMolDescriptors.CalcTPSA"
|
| 38 |
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},
|
| 39 |
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"skipped_by_reason": {
|
| 40 |
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"coordinates_shape": 77717,
|
| 41 |
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"disconnected_heavy_graph": 1
|
| 42 |
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},
|
| 43 |
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"source_file_error_samples": [],
|
| 44 |
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"source_file_errors": {},
|
| 45 |
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"source_processed": {
|
| 46 |
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"raw_zinc": 100068096
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| 47 |
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},
|
| 48 |
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"source_written": {
|
| 49 |
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"raw_zinc": 20000000
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| 50 |
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},
|
| 51 |
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"split": "all accepted records assigned to train",
|
| 52 |
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"started_at_epoch": 1787025901.3424318,
|
| 53 |
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"total_examples": 20000000,
|
| 54 |
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"train_examples": 20000000,
|
| 55 |
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"val_examples": 0,
|
| 56 |
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"validation": {
|
| 57 |
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"selfies_roundtrip_every": 10000,
|
| 58 |
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"smoke_test": false
|
| 59 |
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},
|
| 60 |
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"workers": 192
|
| 61 |
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}
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shard_2/train.lmdb
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a148d129f64ad5c50fae4edf6def3439e6c2083da3c297428c68114b6d7b112b
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| 3 |
+
size 86744469504
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shard_3/metadata.json
ADDED
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@@ -0,0 +1,66 @@
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| 1 |
+
{
|
| 2 |
+
"base_registry_unique": 19999982,
|
| 3 |
+
"base_seen_lmdb": "/scratch/shai/data_20m_selfies_original_cartesian_shards/selfies_seen.lmdb",
|
| 4 |
+
"conformers_per_molecule": 10,
|
| 5 |
+
"coordinate_contract": "coordinates[:, i, :] matches atom i after SELFIES decode and RDKit parse",
|
| 6 |
+
"coordinate_space": "original RDKit Cartesian coordinates; atom-axis permutation only",
|
| 7 |
+
"discarded_after_split_filled": 0,
|
| 8 |
+
"duplicate_selfies_in_base_rejected": 2,
|
| 9 |
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"duplicate_selfies_in_shard_rejected": 59626,
|
| 10 |
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"elapsed_seconds": 5763.920112133026,
|
| 11 |
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"finished_at_epoch": 1787188326.67951,
|
| 12 |
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"local_registry_digest_entries": 20000000,
|
| 13 |
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"local_registry_extra_entries_from_resume": 0,
|
| 14 |
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"local_registry_unique": 20000000,
|
| 15 |
+
"molecular_property_contract": {
|
| 16 |
+
"calculated_from": "canonical heavy-atom molecule represented by smi; standard implicit hydrogens are included by RDKit",
|
| 17 |
+
"molecular_weight_kind": "average molecular weight, not exact isotope mass",
|
| 18 |
+
"rdkit_version": "2025.03.6",
|
| 19 |
+
"sa_score_implementation": "RDKit Contrib SA_Score/sascorer.py"
|
| 20 |
+
},
|
| 21 |
+
"partition_count": 5,
|
| 22 |
+
"partition_index": 2,
|
| 23 |
+
"partition_rejected": 4404048,
|
| 24 |
+
"raw_slices": [
|
| 25 |
+
3,
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| 26 |
+
4,
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| 27 |
+
5,
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| 28 |
+
1,
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| 29 |
+
2
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| 30 |
+
],
|
| 31 |
+
"record_format": {
|
| 32 |
+
"atoms": "heavy-atom symbols in decoded SELFIES atom order",
|
| 33 |
+
"coordinates": "float32 ndarray, shape (10, n_heavy, 3)",
|
| 34 |
+
"mol_log_p": "float; RDKit Crippen.MolLogP",
|
| 35 |
+
"molecular_weight": "float; RDKit Descriptors.MolWt",
|
| 36 |
+
"qed": "float; RDKit QED.qed",
|
| 37 |
+
"sa_score": "float; RDKit Contrib SA_Score; 1 is easiest and 10 is hardest",
|
| 38 |
+
"smi": "SELFIES encoding of canonical isomeric heavy-atom SMILES",
|
| 39 |
+
"tpsa": "float; RDKit rdMolDescriptors.CalcTPSA"
|
| 40 |
+
},
|
| 41 |
+
"resume": {
|
| 42 |
+
"enabled": true,
|
| 43 |
+
"resumed_from_train": 18959723,
|
| 44 |
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"resumed_from_val": 0,
|
| 45 |
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"source_records_skipped": 94505600
|
| 46 |
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},
|
| 47 |
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"skipped_by_reason": {},
|
| 48 |
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"source_file_error_samples": [],
|
| 49 |
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"source_file_errors": {},
|
| 50 |
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"source_processed": {
|
| 51 |
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"raw_zinc": 5504000
|
| 52 |
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},
|
| 53 |
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"source_written": {
|
| 54 |
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"raw_zinc": 1040277
|
| 55 |
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},
|
| 56 |
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"split": "all accepted records assigned to train",
|
| 57 |
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"started_at_epoch": 1787182562.759398,
|
| 58 |
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"total_examples": 20000000,
|
| 59 |
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"train_examples": 20000000,
|
| 60 |
+
"val_examples": 0,
|
| 61 |
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"validation": {
|
| 62 |
+
"selfies_roundtrip_every": 10000,
|
| 63 |
+
"smoke_test": false
|
| 64 |
+
},
|
| 65 |
+
"workers": 192
|
| 66 |
+
}
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shard_3/train.lmdb
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:2816d4c72a03923787240ff8672bf465de43af3198d8aacd6605664e36a32144
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| 3 |
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size 86745681920
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shard_4/metadata.json
ADDED
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@@ -0,0 +1,79 @@
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|
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|
|
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|
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|
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|
| 1 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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| 53 |
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|
| 54 |
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| 55 |
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{
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| 56 |
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| 57 |
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| 58 |
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| 59 |
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| 60 |
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shard_4/train.lmdb
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:af30888477592ab8fdca9c3684308b6a4ce60bcac010db0e7cb298045eeffd70
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size 86746476544
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shard_5/metadata.json
ADDED
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@@ -0,0 +1,79 @@
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| 1 |
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| 3 |
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| 5 |
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| 53 |
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| 57 |
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| 58 |
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| 59 |
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|
| 77 |
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|
| 78 |
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| 79 |
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shard_5/train.lmdb
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:a3eda8b36efad3464bcd0239865857806c1d8ccfc8dab72e8c1abccbc71482b5
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size 86750724096
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