README.md

---
license: cc-by-4.0
task_categories:
- image-to-text
- other
language:
- en
tags:
- electron-microscopy
- stem
- crystal-structure-prediction
- materials-science
- diffusion
pretty_name: STEM2Crystal-Bench
size_categories:
- 1K<n<10K
configs:
- config_name: synthetic
  data_files:
  - split: test
    path: synthetic/metadata.jsonl
- config_name: real_stem_eval5
  data_files:
  - split: test
    path: real_stem_eval5/metadata.jsonl
---

# STEM2Crystal-Bench

STEM2Crystal-Bench is the benchmark for the paper "From Noisy STEM to Crystal Structure: Evidence-Structure CoDiffusion under Composition Constraints" (Chen & You, KDD 2026, Oral), which introduces STEM2Crystal CoDiffusion (SCCD). It evaluates methods that reconstruct a crystal structure from a noisy STEM image when the composition is known. The release has a large synthetic set with controlled noise and a small set of real STEM images, with ground-truth CIFs and a fixed test split.

Code and a live leaderboard: https://github.com/PEESEgroup/STEM2Crystal-Bench

## Contents

The release has two test configs:

| Config | #samples | Source | Role |
|---|---:|---|---|
| `synthetic` | 1021 | Physics-inspired forward pipeline (paper Appendix A.3) applied to curated 2D slab prototypes from **C2DB + MC2D** | Primary evaluation used in paper Table 1 under three noise regimes (low / mid / high) |
| `real_stem_eval5` | 5 | Real, open-licensed atomic-resolution STEM images of **2D monolayer materials**, paired with **single-layer (monolayer) ground-truth CIFs** | Out-of-distribution real-microscopy probe (paper §5.4, Table 2) |

## Folder structure

```
STEM2Crystal-Bench/
├── README.md
├── LICENSE                        # CC BY 4.0
├── synthetic/
│   ├── cifs/                      # 1021 ground-truth CIFs (C2DB + MC2D)
│   ├── images/
│   │   ├── low/                   # 3063 images (1021×3 views), low shot noise
│   │   ├── mid/                   # 3063 images, medium noise
│   │   └── high/                  # 3063 images, high noise
│   ├── masks/                     # atom-position target masks
│   ├── split.json                 # test split IDs (same as paper §5)
│   └── metadata.jsonl             # per-sample lattice/formula/SG
└── real_stem_eval5/
    ├── cifs/                      # 5 COD ground-truth CIFs
    ├── images/                    # 5 real experimental STEM PNGs
    └── metadata.jsonl             # per-sample with source attribution
```

All images in `synthetic/` are resized to **256×256** (the input size used by SCCD and baselines). The full-resolution abTEM output (1286×866 per image, ≈88 GB total) is not redistributed here; the simulation recipe is released with the paper's code.

## Loading

```python
from datasets import load_dataset

synth = load_dataset("gary23ai/STEM2Crystal-Bench", "synthetic", split="test")
real  = load_dataset("gary23ai/STEM2Crystal-Bench", "real_stem_eval5", split="test")
```

Each sample exposes `mp_id`, `formula`, lattice parameters (`a, b, c, alpha, beta, gamma`), `space_group`, and per-noise image paths.

## `real_stem_eval5/` config — data sources

The **5 real experimental samples** are all **genuine 2D monolayer materials** (4 transition-metal dichalcogenides spanning Mo/W × S/Se/Te, plus graphene), assembled as an out-of-distribution real-microscopy probe. Each image is redistributed here **only because the original source is open-licensed (CC BY 4.0 or CC BY 3.0)**; the ground truth is the **single-layer (monolayer) structure**, so a 2D-slab model can match it without prototype templating. We explicitly acknowledge the original authors below.

| # | sid | Material | Phase | Image source | Source paper | DOI | License |
|---|---|---|---|---|---|---|---|
| 1 | `real01_MoTe2_monolayer` | monolayer 2H-MoTe₂ | hexagonal P-6m2 (monolayer) | [Zenodo 5520169](https://zenodo.org/record/5520169) | Guo et al., *npj Comput Mater* (2021) | [10.1038/s41524-021-00642-1](https://doi.org/10.1038/s41524-021-00642-1) | CC BY 4.0 |
| 2 | `real02_WSe2_monolayer` | monolayer 2H-WSe₂ | hexagonal P-6m2 (monolayer) | [Zenodo 7696721](https://zenodo.org/record/7696721) | Tan et al., *npj Comput Mater* (2023) | [10.1038/s41524-023-01042-3](https://doi.org/10.1038/s41524-023-01042-3) | CC BY 4.0 |
| 3 | `real03_WS2_monolayer` | monolayer 2H-WS₂ (+S vacancies) | hexagonal P-6m2 (monolayer) | [figshare 25310755](https://figshare.com/articles/dataset/25310755) | Wang et al., *Nat Commun* (2024) | [10.1038/s41467-024-53880-4](https://doi.org/10.1038/s41467-024-53880-4) | CC BY 4.0 |
| 4 | `real04_MoS2_monolayer` | monolayer 1H-MoS₂ | hexagonal P-6m2 | Wikimedia Commons `MoS2_vacancies.jpg` | Hong et al., *Nat Commun* **6** (2015) | [10.1038/ncomms7293](https://doi.org/10.1038/ncomms7293) | CC BY 4.0 |
| 5 | `real05_graphene` | monolayer graphene | honeycomb P6/mmm | Wikimedia Commons `Graphene-TEM.jpg` | Gass et al., *Nat Nanotechnol* **3** (2008) | [10.1038/nnano.2008.280](https://doi.org/10.1038/nnano.2008.280) | CC BY 3.0 |

**Ground-truth CIFs** are the single-layer (monolayer) structures (TMD layers derived from their COD bulk entries; MoS₂ and graphene use the canonical monolayer cells). Source paper PDFs are not redistributed; please consult the DOIs above.

## Citation

If you use STEM2Crystal-Bench, please cite our paper (KDD 2026, Oral) **and** the original source
papers for the `real_stem_eval5` images listed above.

```bibtex
@inproceedings{chen2026stem2crystal,
  title     = {From Noisy STEM to Crystal Structure: Evidence-Structure CoDiffusion under Composition Constraints},
  author    = {Chen, Guangyao and You, Fengqi},
  booktitle = {Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)},
  year      = {2026},
  note      = {Oral presentation}
}
```

Code + live leaderboard: https://github.com/PEESEgroup/STEM2Crystal-Bench

## License

- **Benchmark assembly, metadata, splits, synthetic STEM renderings**: CC BY 4.0
- **Ground-truth CIFs** (`synthetic/cifs/`: 764 from C2DB + 257 from MC2D; `real_stem_eval5/cifs/`: monolayer structures): upstream licenses (C2DB is CC BY 4.0, MC2D is CC BY 4.0 via Materials Cloud, COD is public-domain)
- **Real STEM images** (`real_stem_eval5/images/`): CC BY 4.0 (four TMD monolayers) and CC BY 3.0 (graphene), redistributed under the terms of the original open-license sources (Zenodo / figshare / Wikimedia Commons), with full attribution to the source authors in the table above