Replace GuacaMol SELFIES arrays with canonical SMILES tokens

GuacaMol/metadata.json

@@ -2,144 +2,143 @@
   "dataset": "GuacaMol v1 distribution-learning benchmark",
   "upstream": "https://github.com/BenevolentAI/guacamol",
   "license": "ChEMBL CC BY-SA 3.0",
-  "representation": "SELFIES 2.2.0 with default constraints and iodine valence 7",
-  "selfies_version": "2.2.0",
-  "sequence_length": 112,
-  "selfies_alphabet": [
-    "[#Branch1]",
-    "[#Branch2]",
-    "[#C-1]",
-    "[#C]",
-    "[#N+1]",
-    "[#N]",
-    "[#O+1]",
-    "[#S]",
-    "[=B-1]",
-    "[=B]",
-    "[=Branch1]",
-    "[=Branch2]",
-    "[=C-1]",
-    "[=C]",
-    "[=IH2]",
-    "[=I]",
-    "[=N+1]",
-    "[=N-1]",
-    "[=NH1+1]",
-    "[=NH2+1]",
-    "[=N]",
-    "[=O+1]",
-    "[=OH1+1]",
-    "[=O]",
-    "[=PH1]",
-    "[=P]",
-    "[=Ring1]",
-    "[=Ring2]",
-    "[=S+1]",
-    "[=SH1]",
-    "[=S]",
-    "[=Se+1]",
-    "[=Se]",
-    "[=Si]",
-    "[B-1]",
-    "[BH0]",
-    "[BH1-1]",
-    "[BH2-1]",
-    "[BH3-1]",
+  "representation": "canonical-smiles-regex-v1-separate-length",
+  "sequence_length": 100,
+  "smiles_alphabet": [
+    "#",
+    "%10",
+    "%11",
+    "%12",
+    "(",
+    ")",
+    "-",
+    "1",
+    "2",
+    "3",
+    "4",
+    "5",
+    "6",
+    "7",
+    "8",
+    "9",
+    "=",
+    "B",
+    "Br",
+    "C",
+    "Cl",
+    "F",
+    "I",
+    "N",
+    "O",
+    "P",
+    "S",
+    "[B-]",
+    "[BH-]",
+    "[BH2-]",
+    "[BH3-]",
     "[B]",
     "[Br+2]",
-    "[Br-1]",
-    "[Br]",
-    "[Branch1]",
-    "[Branch2]",
-    "[C+1]",
-    "[C-1]",
-    "[CH1+1]",
-    "[CH1-1]",
-    "[CH1]",
-    "[CH2+1]",
+    "[Br-]",
+    "[C+]",
+    "[C-]",
+    "[CH+]",
+    "[CH-]",
+    "[CH2+]",
     "[CH2]",
-    "[C]",
-    "[Cl+1]",
+    "[CH]",
     "[Cl+2]",
     "[Cl+3]",
-    "[Cl-1]",
-    "[Cl]",
-    "[F+1]",
-    "[F-1]",
-    "[F]",
+    "[Cl+]",
+    "[Cl-]",
+    "[F+]",
+    "[F-]",
     "[H]",
-    "[I+1]",
     "[I+2]",
     "[I+3]",
-    "[I-1]",
+    "[I+]",
+    "[I-]",
     "[IH2]",
-    "[I]",
-    "[N+1]",
-    "[N-1]",
-    "[NH0]",
-    "[NH1+1]",
-    "[NH1-1]",
-    "[NH1]",
-    "[NH2+1]",
-    "[NH3+1]",
+    "[N+]",
+    "[N-]",
+    "[NH+]",
+    "[NH-]",
+    "[NH2+]",
+    "[NH3+]",
     "[N]",
-    "[O+1]",
-    "[O-1]",
-    "[OH0]",
-    "[OH1+1]",
+    "[O+]",
+    "[O-]",
+    "[OH+]",
     "[O]",
-    "[P+1]",
-    "[P-1]",
-    "[PH1]",
-    "[PH2+1]",
-    "[P]",
-    "[Ring1]",
-    "[Ring2]",
-    "[S+1]",
-    "[S-1]",
-    "[SH1+1]",
-    "[SH1-1]",
-    "[SH1]",
-    "[S]",
-    "[Se+1]",
-    "[Se-1]",
-    "[SeH1]",
+    "[P+]",
+    "[P-]",
+    "[PH2+]",
+    "[PH]",
+    "[S+]",
+    "[S-]",
+    "[SH+]",
+    "[SH-]",
+    "[SH]",
+    "[Se+]",
+    "[Se-]",
     "[SeH2]",
+    "[SeH]",
     "[Se]",
-    "[Si-1]",
-    "[SiH1-1]",
-    "[SiH1]",
+    "[Si-]",
+    "[SiH-]",
     "[SiH2]",
-    "[Si]"
+    "[SiH]",
+    "[Si]",
+    "[b-]",
+    "[c+]",
+    "[c-]",
+    "[cH+]",
+    "[cH-]",
+    "[n+]",
+    "[n-]",
+    "[nH+]",
+    "[nH]",
+    "[o+]",
+    "[s+]",
+    "[se+]",
+    "[se]",
+    "b",
+    "c",
+    "n",
+    "o",
+    "p",
+    "s"
   ],
   "splits": {
     "train": {
       "examples": 1273104,
       "unique": 1273104,
-      "minimum_smiles_length": 1,
-      "maximum_smiles_length": 100,
-      "minimum_selfies_tokens": 1,
-      "maximum_selfies_tokens": 109,
+      "minimum_smiles_characters": 1,
+      "maximum_smiles_characters": 100,
+      "minimum_tokens": 1,
+      "maximum_tokens": 100,
+      "mean_tokens": 46.55556890874587,
       "source_url": "https://ndownloader.figshare.com/files/13612760",
       "source_md5": "05ad85d871958a05c02ab51a4fde8530"
     },
     "validation": {
       "examples": 79568,
       "unique": 79568,
-      "minimum_smiles_length": 5,
-      "maximum_smiles_length": 100,
-      "minimum_selfies_tokens": 4,
-      "maximum_selfies_tokens": 107,
+      "minimum_smiles_characters": 5,
+      "maximum_smiles_characters": 100,
+      "minimum_tokens": 5,
+      "maximum_tokens": 100,
+      "mean_tokens": 46.4712321536296,
       "source_url": "https://ndownloader.figshare.com/files/13612766",
       "source_md5": "e53db4bff7dc4784123ae6df72e3b1f0"
     },
     "test": {
       "examples": 238706,
       "unique": 238706,
-      "minimum_smiles_length": 3,
-      "maximum_smiles_length": 100,
-      "minimum_selfies_tokens": 1,
-      "maximum_selfies_tokens": 108,
+      "minimum_smiles_characters": 3,
+      "maximum_smiles_characters": 100,
+      "minimum_tokens": 1,
+      "maximum_tokens": 100,
+      "mean_tokens": 46.52964315936759,
       "source_url": "https://ndownloader.figshare.com/files/13612757",
       "source_md5": "677b757ccec4809febd83850b43e1616"
     }

GuacaMol/{validation.npy → test_lengths.npy}

@@ -1,3 +1,3 @@
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-size 8911744
+oid sha256:ac1aa605161c1e54bffadf73d9c05d6cf88b2cac4414b895edc2361818fd0004
+size 238834

GuacaMol/{test.npy → test_tokens.npy}

@@ -1,3 +1,3 @@
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-size 26735200
+oid sha256:aae3ca0b2ed44fbed3a16db8382a9390491379ec4a327a7316cdc1437ed986a0
+size 23870728

GuacaMol/{train.npy → train_lengths.npy}

@@ -1,3 +1,3 @@
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-size 142587776
+oid sha256:ceafd183ab4465e9d29e4c5ea45086ea1bdd9b8f2220501af6f0f86381814c31
+size 1273232

GuacaMol/train_tokens.npy

@@ -0,0 +1,3 @@
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+oid sha256:9f0b4bef46f7c3601831704962695ea83193e3209d1073ca3b196bea1897c96d
+size 127310528

GuacaMol/validation_lengths.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:18dbf08e3ea612a0c9cbf615642a88c6a4355142d4bbe41fc4b655e4726600a8
+size 79696

GuacaMol/validation_tokens.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 7956928

README.md

@@ -20,7 +20,7 @@ protocol.
 | `NavierStokes` | Vorticity fields | Fourier-downsampled train/validation/test arrays |
 | `JetNet30` | Particle clouds | Five-class train/validation/test arrays |
 | `DeepSTARR` | Enhancer sequences | Splits, activities, metadata, and official predictor weights |
-| `GuacaMol` | Drug-like molecules | Official non-overlapping ChEMBL splits as robust SELFIES endpoint arrays |
+| `GuacaMol` | Drug-like molecules | Official non-overlapping ChEMBL splits as canonical-SMILES tokens and exact lengths |
 | `SpeechCommands` | One-second spoken-word waveforms | Official speaker-disjoint train/validation/test arrays and labels |
 
 The analytic spiral and checkerboard benchmarks have no stored dataset; their

manifest.json

@@ -9,8 +9,8 @@
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@@ -33,8 +33,8 @@
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+  "total_files": 40,
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   "files": [
     {
       "path": "DeepSTARR/processed/metadata.json",
@@ -68,23 +68,38 @@
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