| --- |
| license: mit |
| task_categories: |
| - text-generation |
| language: |
| - en |
| tags: |
| - molecules |
| - chemistry |
| - pretraining |
| - graph-llm |
| - smiles |
| pretty_name: EDT-Former Encoder Pretraining Data |
| size_categories: |
| - 10M<n<100M |
| --- |
| |
| # 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](https://www.arxiv.org/abs/2602.02742) · [Code](https://github.com/selmiss/DQ-Former) |
|
|
| ## 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 |
|
|
| ```python |
| from datasets import load_dataset |
| |
| dataset = load_dataset("zihaojing/EDT-Former-pretrain-data") |
| ``` |
|
|
| Or point to it in the EDT-Former config: |
|
|
| ```yaml |
| # 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](https://huggingface.co/datasets/zihaojing/EDT-Former-sft-data) | |
| | Encoder (Stage 1) | [zihaojing/EDT-Former-encoder](https://huggingface.co/zihaojing/EDT-Former-encoder) | |
| | Full Model (Stage 2) | [zihaojing/EDT-Former-model](https://huggingface.co/zihaojing/EDT-Former-model) | |
| | Code | [selmiss/DQ-Former](https://github.com/selmiss/DQ-Former) | |
|
|
| ## Citation |
|
|
| ```bibtex |
| @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} |
| } |
| ``` |
|
|
