README.md

---
dataset_info:
- config_name: ip5-markush
  features:
  - name: id
    dtype: string
  - name: page_image_path
    dtype: string
  - name: annotation
    dtype: string
  - name: cxsmiles_dataset
    dtype: string
  - name: cxsmiles
    dtype: string
  - name: cxsmiles_opt
    dtype: string
  - name: cells
    list:
    - name: bbox
      list: float64
    - name: text
      dtype: string
  - name: page_image
    dtype: image
  splits:
  - name: test
    num_bytes: 84715528
    num_examples: 878
  download_size: 84505277
  dataset_size: 84715528
- config_name: m2s
  features:
  - name: id
    dtype: int64
  - name: image_name
    dtype: string
  - name: page_image
    dtype: image
  - name: annotation
    dtype: string
  - name: cxsmiles_dataset
    dtype: string
  - name: cxsmiles
    dtype: string
  - name: cxsmiles_opt
    dtype: string
  - name: cells
    list:
    - name: bbox
      list: float64
    - name: text
      dtype: string
  splits:
  - name: test
    num_bytes: 18029421
    num_examples: 103
  download_size: 17985733
  dataset_size: 18029421
- config_name: uspto-markush
  features:
  - name: id
    dtype: int64
  - name: image_name
    dtype: string
  - name: page_image
    dtype: image
  - name: annotation
    dtype: string
  - name: cxsmiles_dataset
    dtype: string
  - name: cxsmiles
    dtype: string
  - name: cxsmiles_opt
    dtype: string
  - name: cells
    list:
    - name: bbox
      list: float64
    - name: text
      dtype: string
  splits:
  - name: test
    num_bytes: 5196740
    num_examples: 74
  download_size: 5179068
  dataset_size: 5196740
- config_name: uspto-mol-m-54k
  features:
  - name: id
    dtype: int64
  - name: image_name
    dtype: string
  - name: page_image
    dtype: image
  - name: annotation
    dtype: string
  - name: cxsmiles_dataset
    dtype: string
  - name: cxsmiles
    dtype: string
  - name: cxsmiles_opt
    dtype: string
  - name: cells
    list:
    - name: bbox
      list: float64
    - name: text
      dtype: string
  splits:
  - name: train
    num_bytes: 2707938707
    num_examples: 54785
  - name: test
    num_bytes: 10645945
    num_examples: 200
  download_size: 2675522805
  dataset_size: 2718584652
configs:
- config_name: ip5-markush
  data_files:
  - split: test
    path: ip5-markush/test-*
- config_name: m2s
  data_files:
  - split: test
    path: m2s/test-*
- config_name: uspto-markush
  data_files:
  - split: test
    path: uspto-markush/test-*
- config_name: uspto-mol-m-54k
  data_files:
  - split: train
    path: uspto-mol-m-54k/train-*
  - split: test
    path: uspto-mol-m-54k/test-*
---

# MarkushGrapher 2 Datasets

Datasets for training and evaluating **MarkushGrapher 2**, a model for converting patent Markush structure images into CXSMILES representations.

## Dataset Subsets

| Subset | Train | Test | Description | OCR |
|---|---|---|---|---|
| `uspto-mol-m-54k-new` | 54,785 | 200 | USPTO-MOL-M Markush samples | ChemicalOCR predictions |
| `uspto-markush` | — | 74 | USPTO Markush structures benchmark | Ground Truth OCR |
| `m2s` | — | 103 | Mol2Smiles (M2S) benchmark | Ground Truth OCR |
| `IP5-markush` | — | 878 | IP5 Markush structures benchmark | Ground Truth OCR |

## Features

Each sample contains:

- **`page_image`** — Input patent image (PIL Image, typically 1024×1024)
- **`cells`** — OCR-detected text cells with bounding boxes (`bbox` in normalized coordinates, `text`)
- **`cxsmiles`** — Ground truth CXSMILES representation
- **`cxsmiles_opt`** — Optimized (tokenizer-friendly) CXSMILES representation
- **`cxsmiles_dataset`** — Original CXSMILES from the source dataset
- **`annotation`** — Annotation metadata (used to train model)
- **`image_name`** — Source image filename
- **`id`** — Sample identifier

## Usage

```python
from datasets import load_dataset

# Load a specific subset
dataset = load_dataset("docling-project/MarkushGrapher-2-Datasets", "uspto-mol-m-54k")

# Load a benchmark subset
benchmark = load_dataset("docling-project/MarkushGrapher-2-Datasets", "m2s")
```

## Note

**MarkushGrapher-2** is also trained on the following datasets:

- **Phase 1:** 243k real-world image–SMILES pairs from [MolScribe](https://huggingface.co/yujieq/MolScribe)

- **Phase 2:**
  - 235k synthetically generated image–CXSMILES pairs from [MarkushGrapher-Datasets (v1)](https://huggingface.co/datasets/docling-project/MarkushGrapher-Datasets/viewer/markushgrapher-synthetic-training)
  - 91k samples from [MolParser Dataset](https://huggingface.co/datasets/UniParser/MolParser-7M/viewer/sft_real)
## Citation

If you use this dataset, please cite:

```bibtex
@inproceedings{strohmeyer2026markushgrapher2,
  title     = {MarkushGrapher-2: End-to-end Multimodal Recognition of Chemical Structures},
  author    = {Strohmeyer, Tim and Morin, Lucas and Meijer, Gerhard Ingmar and Weber, Valery and Nassar, Ahmed and Staar, Peter W. J.},
  booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year      = {2026}
}
```


### License

This Dataset is released under the Creative Commons Attribution 4.0 License.