Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding
Paper • 2602.02742 • Published
Datasets:
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cid string | split string | iupac_name string | smiles string | brics_gids list | entropy_gids list | graph_data dict |
|---|---|---|---|---|---|---|
1 | pretrain | 3-acetyloxy-4-(trimethylazaniumyl)butanoate | CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C | [
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1000 | pretrain | 2-amino-1-phenylethanol | C1=CC=C(C=C1)C(CN)O | [
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10000 | pretrain | 3-chloro-1,1,1-trifluoropropane | C(CCl)C(F)(F)F | [
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10000009 | pretrain | N-[(2S,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[(2R,3S,4R,5R)-4,5,6-trihydroxy-2-(hydroxymethyl)oxan-3-yl]oxyoxan-3-yl]acetamide | CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@H]1O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)CO)O)O | [
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10000015 | pretrain | N-[(9S)-5,19-dimethoxy-6-oxo-15,17-dioxatetracyclo[10.7.0.02,8.014,18]nonadeca-1(19),2,4,7,12,14(18)-hexaen-9-yl]acetamide | CC(=O)N[C@H]1CCC2=CC3=C(C(=C2C4=CC=C(C(=O)C=C14)OC)OC)OCO3 | [
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10000052 | pretrain | (1S,4'R,6S,10R,11S)-11-chloro-4'-hydroxy-3',4,5-trimethoxyspiro[7-azatricyclo[4.3.3.01,6]dodec-4-ene-10,5'-cyclopent-2-ene]-1',3-dione | COC1=CC(=O)[C@@]2([C@H]1O)[C@H](C[C@@]34[C@@]2(CCN3)CC(=O)C(=C4OC)OC)Cl | [
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10000195 | pretrain | 2,6-ditert-butyl-4-(4-methoxyphenyl)pyrylium;tetrafluoroborate | [B-](F)(F)(F)F.CC(C)(C)C1=CC(=CC(=[O+]1)C(C)(C)C)C2=CC=C(C=C2)OC | [
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100002 | pretrain | 10,14-dimethyl-5-propan-2-yl-3,6,16-trioxapentacyclo[8.6.1.02,4.04,9.014,17]heptadec-8-ene-7,15-dione | CC(C)C1C23C(O2)C4C5C(C3=CC(=O)O1)(CCCC5(C(=O)O4)C)C | [
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100004 | pretrain | methyl 18-ethyl-8,14-diazapentacyclo[9.5.2.01,9.02,7.014,17]octadeca-2,4,6,9-tetraene-10-carboxylate | CCC1C2CCN3C1C4(CC3)C5=CC=CC=C5NC4=C2C(=O)OC | [
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10000451 | pretrain | 3,5-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-6,7,8-trimethoxychromen-4-one | COC1=C(C=C(C=C1)C2=C(C(=O)C3=C(C(=C(C(=C3O2)OC)OC)OC)O)O)O | [
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10000456 | pretrain | 1'-[2-[4-(trifluoromethyl)phenyl]ethyl]spiro[1H-3,1-benzoxazine-4,4'-piperidine]-2-one | C1CN(CCC12C3=CC=CC=C3NC(=O)O2)CCC4=CC=C(C=C4)C(F)(F)F | [
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10000469 | pretrain | [(1R,2R,4R,9R,11S,13S,14R)-2-hydroxy-5,5,9-trimethyl-17-methylidene-10,16-dioxo-15-oxatetracyclo[11.2.2.01,14.04,9]heptadecan-11-yl] acetate | CC(=O)O[C@H]1C[C@@H]2[C@@H]3[C@](O3)([C@@H](C[C@H]4[C@](C1=O)(CCCC4(C)C)C)O)C(=O)C2=C | [
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End of preview.
EDT-Former Encoder Pretraining Data
Pretraining corpus for the EDT-Former Stage 1 encoder, as described in the ICLR 2026 paper:
Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding Zihao Jing, Qiuhao Zeng, Ruiyi Fang, Yan Sun, Boyu Wang, Pingzhao Hu ICLR 2026 · Paper · Code
Dataset Description
This dataset is used to train the Stage 1 EDT-Former encoder, which learns to align molecular graph representations with text. It is derived from PubChem molecules annotated with BRICS fragment IDs and entropy-guided graph IDs.
Data Format
Each split is stored as a JSONL file where each line is a JSON object representing one molecule-text pair, including graph features, SMILES, and associated text descriptions.
| Split | File | Size |
|---|---|---|
| Train | train.jsonl |
~12 GB |
| Validation | val.jsonl |
~37 MB |
| Test | test.jsonl |
~78 MB |
Usage
from datasets import load_dataset
dataset = load_dataset("zihaojing/EDT-Former-pretrain-data")
Or point to it in the EDT-Former config:
# configs/stage1_dqw2d/data_config_preprocessed.yaml
use_preprocessed: true
preprocessed_data: zihaojing/EDT-Former-pretrain-data
Related Resources
| Resource | Link |
|---|---|
| SFT Data | zihaojing/EDT-Former-sft-data |
| Encoder (Stage 1) | zihaojing/EDT-Former-encoder |
| Full Model (Stage 2) | zihaojing/EDT-Former-model |
| Code | selmiss/DQ-Former |
Citation
@inproceedings{jing2026edtformer,
title={Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding},
author={Jing, Zihao and Zeng, Qiuhao and Fang, Ruiyi and Sun, Yan and Wang, Boyu and Hu, Pingzhao},
booktitle={International Conference on Learning Representations (ICLR)},
year={2026}
}
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