# End-to-End Subgraph Detection with GraphDETR

arXiv: https://arxiv.org/abs/2606.06364 · HTML: https://mlsanity.com/paper/2606.06364/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 37 references that are in the map.
- First posted on arXiv 4 Jun 2026.

## Builds on (most cited first, 20 of 20)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection](https://mlsanity.com/paper/2203.03605/) (2022)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [Residual Gated Graph ConvNets](https://mlsanity.com/paper/1711.07553/) (2017)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [Graph Matching Networks for Learning the Similarity of Graph Structured Objects](https://mlsanity.com/paper/1904.12787/) (2019)
- [Structure-Aware Transformer for Graph Representation Learning](https://mlsanity.com/paper/2202.03036/) (2022)
- [SimGNN: A Neural Network Approach to Fast Graph Similarity Computation](https://mlsanity.com/paper/1808.05689/) (2018)
- [Neural Subgraph Matching](https://mlsanity.com/paper/2007.03092/) (2020)
- [Walking Out of the Weisfeiler Leman Hierarchy: Graph Learning Beyond Message Passing](https://mlsanity.com/paper/2102.08786/) (2021)
- [Anonymous Walk Embeddings](https://mlsanity.com/paper/1805.11921/) (2018)
- [Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence](https://mlsanity.com/paper/2502.09263/) (2025)
- [Learning Long Range Dependencies on Graphs via Random Walks](https://mlsanity.com/paper/2406.03386/) (2024)

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

- [GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem](https://mlsanity.com/paper/2606.29161/) (2026)

## Abstract (arXiv)

Subgraph detection seeks to identify whether and where instances of query patterns occur within a larger graph. This problem is fundamental across scientific domains and is closely related to subgraph isomorphism, which is NP-complete, limiting combinatorial approaches to small patterns or moderately sized graphs. We introduce GraphDETR, a deep learning framework that formulates subgraph detection as a set prediction problem, analogous to DETR in object detection. GraphDETR encodes the target graph with a graph neural network, and employs a fixed set of learnable query vectors, decoded via a transformer decoder, to predict all pattern occurrences jointly in a single forward pass. This is enabled by training the model end-to-end with bipartite matching. Unlike traditional combinatorial methods that only solve exact structural matching, GraphDETR naturally extends to approximate matching, enabling detection beyond exact pattern correspondence. Empirically, we show that GraphDETR can detect diverse patterns, such as molecular structures, cycles, cliques, and fuzzy patterns of up to 50 nodes, in target graphs with up to 1000 nodes. We further evaluate on molecular functional group detection over the ChEMBL dataset, where GraphDETR predicts the complete set of functional groups per molecule, achieving a strong performance of AP100 = 91.2.