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Model: kojima-lab/molcrawl-compounds-guacamol-gpt2-small Source: Original Platform
2026-06-09 19:07:20 +08:00
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--- a/README.md
+++ b/README.md
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+---
+license: apache-2.0
+tags:
+- pytorch
+- gpt2
+- molecule-compound
+pipeline_tag: text-generation
+---
+
+# molcrawl-compounds-guacamol-gpt2-small
+
+## Model Description
+
+GPT-2 small (124M parameters) fine-tuned on [GuacaMol](https://github.com/BenevolentAI/guacamol) SMILES data, starting from the `molcrawl-compounds-gpt2-small` pre-trained model.
+
+The tokenizer is a character-level BPE tokenizer (vocab_size=612). Input SMILES strings should be passed **without** spaces. The `[SEP]` token (id=13) is used as the end-of-sequence marker.
+
+## Datasets
+
+- **GuacaMol**: [https://github.com/BenevolentAI/guacamol](https://github.com/BenevolentAI/guacamol) (Fine-tuning dataset)
+
+- **Model Type**: gpt2
+- **Data Type**: Molecule/Compound
+- **Training Date**: 2026-04-24
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+import torch
+
+model = AutoModelForCausalLM.from_pretrained("kojima-lab/molcrawl-compounds-guacamol-gpt2-small")
+tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-compounds-guacamol-gpt2-small")
+
+# Generate SMILES string
+prompt = "CC(=O)O"
+input_ids = tokenizer.encode(prompt, return_tensors="pt")
+with torch.no_grad():
+    output_ids = model.generate(
+        input_ids,
+        max_new_tokens=50,
+        do_sample=True,
+        temperature=0.8,
+        eos_token_id=tokenizer.convert_tokens_to_ids("[SEP]"),  # [SEP] is EOS for compounds
+        pad_token_id=0,
+    )
+print(tokenizer.decode(output_ids[0], skip_special_tokens=True))
+
+```
+
+## Source Code
+
+Training pipeline, configuration files, and data preparation scripts are
+available in the MolCrawl GitHub repository:
+[https://github.com/mmai-framework-lab/MolCrawl](https://github.com/mmai-framework-lab/MolCrawl)
+
+## License
+
+This model is released under the APACHE-2.0 license.
+
+## Citation
+
+If you use this model, please cite:
+
+```bibtex
+@misc{molcrawl_compounds_guacamol_gpt2_small,
+  title={molcrawl-compounds-guacamol-gpt2-small},
+  author={{RIKEN}},
+  year={2026},
+  publisher={{Hugging Face}},
+  url={{https://huggingface.co/kojima-lab/molcrawl-compounds-guacamol-gpt2-small}}
+}
+```
--- a/config.json
+++ b/config.json
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+{
+  "architectures": [
+    "GPT2LMHeadModel"
+  ],
+  "model_type": "gpt2",
+  "vocab_size": 612,
+  "n_positions": 1024,
+  "n_ctx": 1024,
+  "n_embd": 768,
+  "n_layer": 12,
+  "n_head": 12,
+  "n_inner": 3072,
+  "activation_function": "gelu_new",
+  "resid_pdrop": 0.0,
+  "embd_pdrop": 0.0,
+  "attn_pdrop": 0.0,
+  "layer_norm_epsilon": 1e-05,
+  "initializer_range": 0.02,
+  "use_cache": true,
+  "bos_token_id": 0,
+  "eos_token_id": 0,
+  "transformers_version": "4.0.0",
+  "_name_or_path": "riken-gpt2",
+  "_riken_model_args": {
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+    "n_head": 12,
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+    "bias": false,
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+    "dropout": 0.0
+  },
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+}
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+  "_from_model_config": true,
+  "bos_token_id": 0,
+  "eos_token_id": 0,
+  "transformers_version": "4.45.1"
+}
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+      "[SbH2]": 448,
+      "[Ag+3]": 449,
+      "%24": 450,
+      "[18O]": 451,
+      "[PH4]": 452,
+      "[Os+2]": 453,
+      "[Na-]": 454,
+      "[Sb+2]": 455,
+      "[V+4]": 456,
+      "[Ho+3]": 457,
+      "[68Ga]": 458,
+      "[PH-]": 459,
+      "[Bi+2]": 460,
+      "[Ce+2]": 461,
+      "[Pd+3]": 462,
+      "[99Tc]": 463,
+      "[13C@@H]": 464,
+      "[Fe+6]": 465,
+      "[c]": 466,
+      "[GeH2]": 467,
+      "[10B]": 468,
+      "[Cu+3]": 469,
+      "[Mo+2]": 470,
+      "[Cr+]": 471,
+      "[Pd+4]": 472,
+      "[Dy]": 473,
+      "[AsH]": 474,
+      "[Ba+]": 475,
+      "[SeH2]": 476,
+      "[In+]": 477,
+      "[TeH2]": 478,
+      "[BrH+]": 479,
+      "[14cH]": 480,
+      "[W+]": 481,
+      "[13C@H]": 482,
+      "[AsH2]": 483,
+      "[In+2]": 484,
+      "[N+2]": 485,
+      "[N@@H+]": 486,
+      "[SbH]": 487,
+      "[60Co]": 488,
+      "[AsH4+]": 489,
+      "[AsH3]": 490,
+      "[18OH]": 491,
+      "[Ru-2]": 492,
+      "[Na-2]": 493,
+      "[CuH2]": 494,
+      "[31P]": 495,
+      "[Ti+5]": 496,
+      "[35S]": 497,
+      "[P@@H]": 498,
+      "[ArH]": 499,
+      "[Co+]": 500,
+      "[Zr-2]": 501,
+      "[BH2-]": 502,
+      "[131I]": 503,
+      "[SH5]": 504,
+      "[VH]": 505,
+      "[B+2]": 506,
+      "[Yb+2]": 507,
+      "[14C@H]": 508,
+      "[211At]": 509,
+      "[NH3+2]": 510,
+      "[IrH]": 511,
+      "[IrH2]": 512,
+      "[Rh-]": 513,
+      "[Cr-]": 514,
+      "[Sb+]": 515,
+      "[Ni+3]": 516,
+      "[TaH3]": 517,
+      "[Tl+2]": 518,
+      "[64Cu]": 519,
+      "[Tc]": 520,
+      "[Cd+]": 521,
+      "[1H]": 522,
+      "[15nH]": 523,
+      "[AlH2+]": 524,
+      "[FH+2]": 525,
+      "[BiH3]": 526,
+      "[Ru-]": 527,
+      "[Mo+6]": 528,
+      "[AsH+]": 529,
+      "[BaH2]": 530,
+      "[BaH]": 531,
+      "[Fe+4]": 532,
+      "[229Th]": 533,
+      "[Th+4]": 534,
+      "[As+3]": 535,
+      "[NH+3]": 536,
+      "[P@H]": 537,
+      "[Li-]": 538,
+      "[7NaH]": 539,
+      "[Bi+]": 540,
+      "[PtH+2]": 541,
+      "[p-]": 542,
+      "[Re+5]": 543,
+      "[NiH]": 544,
+      "[Ni-]": 545,
+      "[Xe+]": 546,
+      "[Ca+]": 547,
+      "[11c]": 548,
+      "[Rh+4]": 549,
+      "[AcH]": 550,
+      "[HeH]": 551,
+      "[Sc+2]": 552,
+      "[Mn+]": 553,
+      "[UH]": 554,
+      "[14CH2]": 555,
+      "[SiH4+]": 556,
+      "[18OH2]": 557,
+      "[Ac-]": 558,
+      "[Re+4]": 559,
+      "[118Sn]": 560,
+      "[153Sm]": 561,
+      "[P+2]": 562,
+      "[9CH]": 563,
+      "[9CH3]": 564,
+      "[Y-]": 565,
+      "[NiH2]": 566,
+      "[Si+2]": 567,
+      "[Mn+6]": 568,
+      "[ZrH2]": 569,
+      "[C-2]": 570,
+      "[Bi+5]": 571,
+      "[24NaH]": 572,
+      "[Fr]": 573,
+      "[15CH]": 574,
+      "[Se+]": 575,
+      "[At]": 576,
+      "[P-3]": 577,
+      "[124I-]": 578,
+      "[CuH2-]": 579,
+      "[Nb+4]": 580,
+      "[Nb+3]": 581,
+      "[MgH]": 582,
+      "[Ir+4]": 583,
+      "[67Ga+3]": 584,
+      "[67Ga]": 585,
+      "[13N]": 586,
+      "[15OH2]": 587,
+      "[2NH]": 588,
+      "[Ho]": 589,
+      "[Cn]": 590,
+      "[0*]": 591,
+      "[1*]": 592,
+      "[2*]": 593,
+      "[3*]": 594,
+      "[4*]": 595,
+      "[5*]": 596,
+      "[6*]": 597,
+      "[7*]": 598,
+      "[8*]": 599,
+      "[9*]": 600,
+      "[10*]": 601,
+      "[11*]": 602,
+      "[12*]": 603,
+      "[13*]": 604,
+      "[14*]": 605,
+      "[15*]": 606,
+      "[16*]": 607,
+      "[17*]": 608,
+      "[18*]": 609,
+      "[19*]": 610,
+      "[20*]": 611
+    },
+    "unk_token": "[UNK]"
+  }
+}
--- a/tokenizer_config.json
+++ b/tokenizer_config.json
@@ -0,0 +1,52 @@
+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "11": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "12": {
+      "content": "[CLS]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "13": {
+      "content": "[SEP]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "14": {
+      "content": "[MASK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "clean_up_tokenization_spaces": false,
+  "cls_token": "[CLS]",
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "tokenizer_class": "PreTrainedTokenizerFast",
+  "unk_token": "[UNK]"
+}
--- a/training_args.json
+++ b/training_args.json
@@ -0,0 +1,17 @@
+{
+  "iteration": 2000,
+  "best_val_loss": 0.031413231045007706,
+  "early_stopping_counter": 1,
+  "learning_rate": 1e-05,
+  "batch_size": 8,
+  "block_size": 1024,
+  "model_args": {
+    "n_layer": 12,
+    "n_head": 12,
+    "n_embd": 768,
+    "block_size": 1024,
+    "bias": false,
+    "vocab_size": 612,
+    "dropout": 0.0
+  }
+}
--- a/vocab.txt
+++ b/vocab.txt
@@ -0,0 +1,612 @@
+[PAD]
+[unused1]
+[unused2]
+[unused3]
+[unused4]
+[unused5]
+[unused6]
+[unused7]
+[unused8]
+[unused9]
+[unused10]
+[UNK]
+[CLS]
+[SEP]
+[MASK]
+c
+C
+(
+)
+O
+1
+2
+=
+N
+.
+n
+3
+F
+Cl
+>>
+~
+-
+4
+[C@H]
+S
+[C@@H]
+[O-]
+Br
+#
+/
+[nH]
+[N+]
+s
+5
+o
+P
+[Na+]
+[Si]
+I
+[Na]
+[Pd]
+[K+]
+[K]
+[P]
+B
+[C@]
+[C@@]
+[Cl-]
+6
+[OH-]
+\
+[N-]
+[Li]
+[H]
+[2H]
+[NH4+]
+[c-]
+[P-]
+[Cs+]
+[Li+]
+[Cs]
+[NaH]
+[H-]
+[O+]
+[BH4-]
+[Cu]
+7
+[Mg]
+[Fe+2]
+[n+]
+[Sn]
+[BH-]
+[Pd+2]
+[CH]
+[I-]
+[Br-]
+[C-]
+[Zn]
+[B-]
+[F-]
+[Al]
+[P+]
+[BH3-]
+[Fe]
+[C]
+[AlH4]
+[Ni]
+[SiH]
+8
+[Cu+2]
+[Mn]
+[AlH]
+[nH+]
+[AlH4-]
+[O-2]
+[Cr]
+[Mg+2]
+[NH3+]
+[S@]
+[Pt]
+[Al+3]
+[S@@]
+[S-]
+[Ti]
+[Zn+2]
+[PH]
+[NH2+]
+[Ru]
+[Ag+]
+[S+]
+[I+3]
+[NH+]
+[Ca+2]
+[Ag]
+9
+[Os]
+[Se]
+[SiH2]
+[Ca]
+[Ti+4]
+[Ac]
+[Cu+]
+[S]
+[Rh]
+[Cl+3]
+[cH-]
+[Zn+]
+[O]
+[Cl+]
+[SH]
+[H+]
+[Pd+]
+[se]
+[PH+]
+[I]
+[Pt+2]
+[C+]
+[Mg+]
+[Hg]
+[W]
+[SnH]
+[SiH3]
+[Fe+3]
+[NH]
+[Mo]
+[CH2+]
+%10
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+[CH2]
+[n-]
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+[NH-]
+[Co]
+[I+]
+[PH2]
+[Pt+4]
+[Ce]
+[B]
+[Sn+2]
+[Ba+2]
+%11
+[Fe-3]
+[18F]
+[SH-]
+[Pb+2]
+[Os-2]
+[Zr+4]
+[N]
+[Ir]
+[Bi]
+[Ni+2]
+[P@]
+[Co+2]
+[s+]
+[As]
+[P+3]
+[Hg+2]
+[Yb+3]
+[CH-]
+[Zr+2]
+[Mn+2]
+[CH+]
+[In]
+[KH]
+[Ce+3]
+[Zr]
+[AlH2-]
+[OH2+]
+[Ti+3]
+[Rh+2]
+[Sb]
+[S-2]
+%12
+[P@@]
+[Si@H]
+[Mn+4]
+p
+[Ba]
+[NH2-]
+[Ge]
+[Pb+4]
+[Cr+3]
+[Au]
+[LiH]
+[Sc+3]
+[o+]
+[Rh-3]
+%13
+[Br]
+[Sb-]
+[S@+]
+[I+2]
+[Ar]
+[V]
+[Cu-]
+[Al-]
+[Te]
+[13c]
+[13C]
+[Cl]
+[PH4+]
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+[Rh+3]
+[SH+]
+[Bi+3]
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+[La]
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+*
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+[OH]
+[Gd+3]
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+[Si@]
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+[Ga]
+[Sn+4]
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+[Hf]
+[Pr]
+[Y]
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+[Cd]
+[Cr+6]
+[Zr+3]
+[Rh+]
+[CH3]
+[N-3]
+[Hf+2]
+[Th]
+[Sb+3]
+%14
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+[Lu]
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+[Gd]
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+[TeH]
+[Si@@H]
+[Ga+3]
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+[GeH]
+[Br+]
+[Sr]
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+[Sm+2]
+[PH5]
+%16
+[N@@+]
+[Au+3]
+[C-4]
+[Nd]
+[Ti+]
+[IH]
+[N@+]
+[125I]
+[Eu]
+[Sn+3]
+[Nb]
+[Er+3]
+[123I-]
+[14c]
+%17
+[SnH2]
+[YH]
+[Sb+5]
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+[Rb]
+[pH]
+%19
+%20
+[Xe]
+[Ir-]
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+[U+2]
+[Au-]
+%21
+%22
+[Au+]
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+[ClH+]
+b
+[Ti+6]
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+[RuH]
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+%23
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+[64Cu]
+[Tc]
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+[1H]
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+[229Th]
+[Th+4]
+[As+3]
+[NH+3]
+[P@H]
+[Li-]
+[7NaH]
+[Bi+]
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+[p-]
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+[Y-]
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+[ZrH2]
+[C-2]
+[Bi+5]
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+[Fr]
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+[Se+]
+[At]
+[P-3]
+[124I-]
+[CuH2-]
+[Nb+4]
+[Nb+3]
+[MgH]
+[Ir+4]
+[67Ga+3]
+[67Ga]
+[13N]
+[15OH2]
+[2NH]
+[Ho]
+[Cn]
+[0*]
+[1*]
+[2*]
+[3*]
+[4*]
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