Update GuacaMol reduced-character benchmark data

GuacaMol/metadata.json

@@ -2,16 +2,17 @@
   "dataset": "GuacaMol v1 distribution-learning benchmark",
   "upstream": "https://github.com/BenevolentAI/guacamol",
   "license": "ChEMBL CC BY-SA 3.0",
-  "representation": "canonical-smiles-regex-v1-separate-length",
+  "representation": "canonical-smiles-reduced-character-v1-empirical-length",
   "sequence_length": 100,
   "smiles_alphabet": [
     "#",
-    "%10",
-    "%11",
-    "%12",
+    "%",
     "(",
     ")",
+    "+",
     "-",
+    ".",
+    "0",
     "1",
     "2",
     "3",
@@ -22,101 +23,52 @@
     "8",
     "9",
     "=",
+    "A",
     "B",
-    "Br",
     "C",
-    "Cl",
     "F",
+    "H",
     "I",
     "N",
     "O",
     "P",
     "S",
-    "[B-]",
-    "[BH-]",
-    "[BH2-]",
-    "[BH3-]",
-    "[B]",
-    "[Br+2]",
-    "[Br-]",
-    "[C+]",
-    "[C-]",
-    "[CH+]",
-    "[CH-]",
-    "[CH2+]",
-    "[CH2]",
-    "[CH]",
-    "[Cl+2]",
-    "[Cl+3]",
-    "[Cl+]",
-    "[Cl-]",
-    "[F+]",
-    "[F-]",
-    "[H]",
-    "[I+2]",
-    "[I+3]",
-    "[I+]",
-    "[I-]",
-    "[IH2]",
-    "[N+]",
-    "[N-]",
-    "[NH+]",
-    "[NH-]",
-    "[NH2+]",
-    "[NH3+]",
-    "[N]",
-    "[O+]",
-    "[O-]",
-    "[OH+]",
-    "[O]",
-    "[P+]",
-    "[P-]",
-    "[PH2+]",
-    "[PH]",
-    "[S+]",
-    "[S-]",
-    "[SH+]",
-    "[SH-]",
-    "[SH]",
-    "[Se+]",
-    "[Se-]",
-    "[SeH2]",
-    "[SeH]",
-    "[Se]",
-    "[Si-]",
-    "[SiH-]",
-    "[SiH2]",
-    "[SiH]",
-    "[Si]",
-    "[b-]",
-    "[c+]",
-    "[c-]",
-    "[cH+]",
-    "[cH-]",
-    "[n+]",
-    "[n-]",
-    "[nH+]",
-    "[nH]",
-    "[o+]",
-    "[s+]",
-    "[se+]",
-    "[se]",
+    "X",
+    "Y",
+    "Z",
+    "[",
+    "]",
     "b",
     "c",
     "n",
     "o",
     "p",
-    "s"
+    "s",
+    "@",
+    "R",
+    "/",
+    "\\",
+    "E"
   ],
+  "multi_character_reductions": {
+    "Br": "Y",
+    "Cl": "X",
+    "Si": "A",
+    "Se": "Z",
+    "@@": "R",
+    "se": "E"
+  },
+  "length_model": null,
+  "sampling_lengths": "empirical training distribution",
   "splits": {
     "train": {
       "examples": 1273104,
       "unique": 1273104,
       "minimum_smiles_characters": 1,
       "maximum_smiles_characters": 100,
-      "minimum_tokens": 1,
-      "maximum_tokens": 100,
-      "mean_tokens": 46.55556890874587,
+      "minimum_reduced_characters": 1,
+      "maximum_reduced_characters": 100,
+      "mean_reduced_characters": 47.29526181678794,
       "source_url": "https://ndownloader.figshare.com/files/13612760",
       "source_md5": "05ad85d871958a05c02ab51a4fde8530"
     },
@@ -125,9 +77,9 @@
       "unique": 79568,
       "minimum_smiles_characters": 5,
       "maximum_smiles_characters": 100,
-      "minimum_tokens": 5,
-      "maximum_tokens": 100,
-      "mean_tokens": 46.4712321536296,
+      "minimum_reduced_characters": 5,
+      "maximum_reduced_characters": 100,
+      "mean_reduced_characters": 47.21912075206113,
       "source_url": "https://ndownloader.figshare.com/files/13612766",
       "source_md5": "e53db4bff7dc4784123ae6df72e3b1f0"
     },
@@ -136,9 +88,9 @@
       "unique": 238706,
       "minimum_smiles_characters": 3,
       "maximum_smiles_characters": 100,
-      "minimum_tokens": 1,
-      "maximum_tokens": 100,
-      "mean_tokens": 46.52964315936759,
+      "minimum_reduced_characters": 3,
+      "maximum_reduced_characters": 100,
+      "mean_reduced_characters": 47.272288924451,
       "source_url": "https://ndownloader.figshare.com/files/13612757",
       "source_md5": "677b757ccec4809febd83850b43e1616"
     }

GuacaMol/test_lengths.npy

@@ -1,3 +1,3 @@
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GuacaMol/test_tokens.npy

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GuacaMol/train_lengths.npy

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GuacaMol/train_tokens.npy

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GuacaMol/validation_lengths.npy

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GuacaMol/validation_tokens.npy

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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 canonical-SMILES tokens and exact lengths |
+| `GuacaMol` | Drug-like molecules | Official non-overlapping ChEMBL splits as losslessly reduced canonical-SMILES endpoint arrays and 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

@@ -10,7 +10,7 @@
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@@ -34,7 +34,7 @@
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