# Graph Neural Networks for Double-Strand DNA Breaks Prediction

arXiv: https://arxiv.org/abs/2201.01855 · HTML: https://mlsanity.com/paper/2201.01855/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 39 references that are in the map.
- First posted on arXiv 4 Jan 2022.

## Builds on (most cited first, 15 of 15)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks](https://mlsanity.com/paper/1909.01315/) (2019)
- [Search to aggregate neighborhood for graph neural network](https://mlsanity.com/paper/2104.06608/) (2021)
- [Property-Aware Relation Networks for Few-Shot Molecular Property Prediction](https://mlsanity.com/paper/2107.07994/) (2021)
- [Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification](https://mlsanity.com/paper/1711.05859/) (2017)
- [Automated Machine Learning on Graphs: A Survey](https://mlsanity.com/paper/2103.00742/) (2021)
- [Pooling Architecture Search for Graph Classification](https://mlsanity.com/paper/2108.10587/) (2021)
- [Designing the Topology of Graph Neural Networks: A Novel Feature Fusion Perspective](https://mlsanity.com/paper/2112.14531/) (2021)

## Built on by (most cited first, 1 of 1)

- [Graph Property Prediction on Open Graph Benchmark: A Winning Solution by Graph Neural Architecture Search](https://mlsanity.com/paper/2207.06027/) (2022)

## Abstract (arXiv)

Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a graph neural network based method to predict DSBs (GraphDSB), using DNA sequence features and chromosome structure information. In order to improve the expression ability of the model, we introduce Jumping Knowledge architecture and several effective structural encoding methods. The contribution of structural information to the prediction of DSBs is verified by the experiments on datasets from normal human epidermal keratinocytes (NHEK) and chronic myeloid leukemia cell line (K562), and the ablation studies further demonstrate the effectiveness of the designed components in the proposed GraphDSB framework. Finally, we use GNNExplainer to analyze the contribution of node features and topology to DSBs prediction, and proved the high contribution of 5-mer DNA sequence features and two chromatin interaction modes.