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Model: kojima-lab/molcrawl-compounds-guacamol-gpt2-small
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2026-06-09 19:07:20 +08:00
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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}}
}
```

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{
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"GPT2LMHeadModel"
],
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"block_size": 1024,
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"dropout": 0.0
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"[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]"
}
}

52
tokenizer_config.json Normal file
View File

@@ -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]"
}

17
training_args.json Normal file
View File

@@ -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
}
}

612
vocab.txt Normal file
View File

@@ -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
[CH2-]
[CH2]
[n-]
[Ce+4]
[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+]
[SiH4]
[te]
[CH3-]
[S@@+]
[Rh+3]
[SH+]
[Bi+3]
[Br+2]
[La]
[La+3]
[Pt-2]
[N@@]
[PH3+]
[N@]
[Si+4]
[Sr+2]
[Al+]
[Pb]
[SeH]
[Si-]
[V+5]
[Y+3]
[Re]
[Ru+]
[Sm]
*
[3H]
[NH2]
[Ag-]
[13CH3]
[OH+]
[Ru+3]
[OH]
[Gd+3]
[13CH2]
[In+3]
[Si@@]
[Si@]
[Ti+2]
[Sn+]
[Cl+2]
[AlH-]
[Pd-2]
[SnH3]
[B+3]
[Cu-2]
[Nd+3]
[Pb+3]
[13cH]
[Fe-4]
[Ga]
[Sn+4]
[Hg+]
[11CH3]
[Hf]
[Pr]
[Y]
[S+2]
[Cd]
[Cr+6]
[Zr+3]
[Rh+]
[CH3]
[N-3]
[Hf+2]
[Th]
[Sb+3]
%14
[Cr+2]
[Ru+2]
[Hf+4]
[14C]
[Ta]
[Tl+]
[B+]
[Os+4]
[PdH2]
[Pd-]
[Cd+2]
[Co+3]
[S+4]
[Nb+5]
[123I]
[c+]
[Rb+]
[V+2]
[CH3+]
[Ag+2]
[cH+]
[Mn+3]
[Se-]
[As-]
[Eu+3]
[SH2]
[Sm+3]
[IH+]
%15
[OH3+]
[PH3]
[IH2+]
[SH2+]
[Ir+3]
[AlH3]
[Sc]
[Yb]
[15NH2]
[Lu]
[sH+]
[Gd]
[18F-]
[SH3+]
[SnH4]
[TeH]
[Si@@H]
[Ga+3]
[CaH2]
[Tl]
[Ta+5]
[GeH]
[Br+]
[Sr]
[Tl+3]
[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]
[Pr+3]
[Ir+]
[N+3]
[AlH2]
[19F]
%18
[Tb]
[14CH]
[Mo+4]
[Si+]
[BH]
[Be]
[Rb]
[pH]
%19
%20
[Xe]
[Ir-]
[Be+2]
[C+4]
[RuH2]
[15NH]
[U+2]
[Au-]
%21
%22
[Au+]
[15n]
[Al+2]
[Tb+3]
[15N]
[V+3]
[W+6]
[14CH3]
[Cr+4]
[ClH+]
b
[Ti+6]
[Nd+]
[Zr+]
[PH2+]
[Fm]
[N@H+]
[RuH]
[Dy+3]
%23
[Hf+3]
[W+4]
[11C]
[13CH]
[Er]
[124I]
[LaH]
[F]
[siH]
[Ga+]
[Cm]
[GeH3]
[IH-]
[U+6]
[SeH+]
[32P]
[SeH-]
[Pt-]
[Ir+2]
[se+]
[U]
[F+]
[BH2]
[As+]
[Cf]
[ClH2+]
[Ni+]
[TeH3]
[SbH2]
[Ag+3]
%24
[18O]
[PH4]
[Os+2]
[Na-]
[Sb+2]
[V+4]
[Ho+3]
[68Ga]
[PH-]
[Bi+2]
[Ce+2]
[Pd+3]
[99Tc]
[13C@@H]
[Fe+6]
[c]
[GeH2]
[10B]
[Cu+3]
[Mo+2]
[Cr+]
[Pd+4]
[Dy]
[AsH]
[Ba+]
[SeH2]
[In+]
[TeH2]
[BrH+]
[14cH]
[W+]
[13C@H]
[AsH2]
[In+2]
[N+2]
[N@@H+]
[SbH]
[60Co]
[AsH4+]
[AsH3]
[18OH]
[Ru-2]
[Na-2]
[CuH2]
[31P]
[Ti+5]
[35S]
[P@@H]
[ArH]
[Co+]
[Zr-2]
[BH2-]
[131I]
[SH5]
[VH]
[B+2]
[Yb+2]
[14C@H]
[211At]
[NH3+2]
[IrH]
[IrH2]
[Rh-]
[Cr-]
[Sb+]
[Ni+3]
[TaH3]
[Tl+2]
[64Cu]
[Tc]
[Cd+]
[1H]
[15nH]
[AlH2+]
[FH+2]
[BiH3]
[Ru-]
[Mo+6]
[AsH+]
[BaH2]
[BaH]
[Fe+4]
[229Th]
[Th+4]
[As+3]
[NH+3]
[P@H]
[Li-]
[7NaH]
[Bi+]
[PtH+2]
[p-]
[Re+5]
[NiH]
[Ni-]
[Xe+]
[Ca+]
[11c]
[Rh+4]
[AcH]
[HeH]
[Sc+2]
[Mn+]
[UH]
[14CH2]
[SiH4+]
[18OH2]
[Ac-]
[Re+4]
[118Sn]
[153Sm]
[P+2]
[9CH]
[9CH3]
[Y-]
[NiH2]
[Si+2]
[Mn+6]
[ZrH2]
[C-2]
[Bi+5]
[24NaH]
[Fr]
[15CH]
[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*]
[5*]
[6*]
[7*]
[8*]
[9*]
[10*]
[11*]
[12*]
[13*]
[14*]
[15*]
[16*]
[17*]
[18*]
[19*]
[20*]