graphs-datasets/MD17-naphthalene

---
licence: unknown
task_categories:
- graph-ml
---

# Dataset Card for naphthalene

## Table of Contents
- [Table of Contents](#table-of-contents)
- [Dataset Description](#dataset-description)
- [Dataset Summary](#dataset-summary)
- [Supported Tasks and Leaderboards](#supported-tasks-and-leaderboards)
- [External Use](#external-use)
- [PyGeometric](#pygeometric)
- [Dataset Structure](#dataset-structure)
- [Data Properties](#data-properties)
- [Data Fields](#data-fields)
- [Data Splits](#data-splits)
- [Additional Information](#additional-information)
- [Licensing Information](#licensing-information)
- [Citation Information](#citation-information)
- [Contributions](#contributions)

## Dataset Description
- **[Homepage](http://www.sgdml.org/#datasets)**
- **Paper:**: (see citation)

### Dataset Summary
The `naphthalene` dataset is a molecular dynamics (MD) dataset. The total energy and force labels for each dataset were computed using the PBE+vdW-TS electronic structure method. All geometries are in Angstrom, energies and forces are given in kcal/mol and kcal/mol/A respectively.

### Supported Tasks and Leaderboards
`naphthalene` should be used for organic molecular property prediction, a regression task on 1 property. The score used is Mean absolute errors (in meV) for energy prediction.

## External Use
### PyGeometric
To load in PyGeometric, do the following:

```python
from datasets import load_dataset

from torch_geometric.data import Data
from torch_geometric.loader import DataLoader

dataset_hf = load_dataset("graphs-datasets/<mydataset>")
# For the train set (replace by valid or test as needed)
dataset_pg_list = [Data(graph) for graph in dataset_hf["train"]]
dataset_pg = DataLoader(dataset_pg_list)
```

## Dataset Structure

### Data Properties
| property | value |
|---|---|
| scale | big |
| #graphs | 226255 |
| average #nodes | 18.0 |
| average #edges | 254.73246234354005 |

### Data Fields

Each row of a given file is a graph, with:
- `node_feat` (list: #nodes x #node-features): nodes
- `edge_index` (list: 2 x #edges): pairs of nodes constituting edges
- `edge_attr` (list: #edges x #edge-features): for the aforementioned edges, contains their features
- `y` (list: #labels): contains the number of labels available to predict
- `num_nodes` (int): number of nodes of the graph

### Data Splits

This data is not split, and should be used with cross validation. It comes from the PyGeometric version of the dataset.

## Additional Information

### Licensing Information
The dataset has been released under license unknown.

### Citation Information
```
@inproceedings{Morris+2020,
title={TUDataset: A collection of benchmark datasets for learning with graphs},
author={Christopher Morris and Nils M. Kriege and Franka Bause and Kristian Kersting and Petra Mutzel and Marion Neumann},
booktitle={ICML 2020 Workshop on Graph Representation Learning and Beyond (GRL+ 2020)},
archivePrefix={arXiv},
eprint={2007.08663},
url={www.graphlearning.io},
year={2020}
}
```

```

@article{Chmiela_2017,
doi = {10.1126/sciadv.1603015},
url = {https://doi.org/10.1126%2Fsciadv.1603015},
year = 2017,
month = {may},
publisher = {American Association for the Advancement of Science ({AAAS})},
volume = {3},
number = {5},
author = {Stefan Chmiela and Alexandre Tkatchenko and Huziel E. Sauceda and Igor Poltavsky and Kristof T. Schütt and Klaus-Robert Müller},
title = {Machine learning of accurate energy-conserving molecular force fields},
journal = {Science Advances}
}

```

原始信息汇总

数据集概述

数据集名称

• naphthalene

数据集类型

• 分子动力学（MD）数据集

数据集用途

• 用于有机分子属性预测，具体为回归任务，预测单一属性

数据集特征

• 总能量和力标签使用PBE+vdW-TS电子结构方法计算
• 几何结构单位为Angstrom，能量单位为kcal/mol，力单位为kcal/mol/A

评估指标

• 使用平均绝对误差（meV）评估能量预测

数据集结构

• 数据属性

  • 规模：大
  • 图数量：226255
  • 平均节点数：18.0
  • 平均边数：254.73246234354005

• 数据字段

  • node_feat：节点特征列表
  • edge_index：边索引列表
  • edge_attr：边特征列表
  • y：标签列表
  • num_nodes：节点数量

数据集使用

• 建议使用交叉验证，数据未分割

许可证信息

• 许可证：未知

引用信息

• 参考文献：Morris+2020 和 Chmiela_2017