# End-to-End Cell Detection via Instance-aware Graph Modeling

arXiv: https://arxiv.org/abs/2609.15354 · HTML: https://mlsanity.com/paper/2609.15354/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 40 of its 65 references that are in the map.
- First posted on arXiv 14 Sep 2026.

## Builds on (most cited first, 30 of 40)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [Generalized Intersection over Union: A Metric and A Loss for Bounding Box Regression](https://mlsanity.com/paper/1902.09630/) (2019)
- [DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection](https://mlsanity.com/paper/2203.03605/) (2022)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [HiPPO: Recurrent Memory with Optimal Polynomial Projections](https://mlsanity.com/paper/2008.07669/) (2020)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [DAB-DETR: Dynamic Anchor Boxes are Better Queries for DETR](https://mlsanity.com/paper/2201.12329/) (2022)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [DETRs with Collaborative Hybrid Assignments Training](https://mlsanity.com/paper/2211.12860/) (2022)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)
- [Cell Detection with Star-convex Polygons](https://mlsanity.com/paper/1806.03535/) (2018)
- [Dense Distinct Query for End-to-End Object Detection](https://mlsanity.com/paper/2303.12776/) (2023)
- [Mitosis domain generalization in histopathology images -- The MIDOG challenge](https://mlsanity.com/paper/2204.03742/) (2022)
- [Micro-Net: A unified model for segmentation of various objects in microscopy images](https://mlsanity.com/paper/1804.08145/) (2018)
- [Attention-Based Transformers for Instance Segmentation of Cells in Microstructures](https://mlsanity.com/paper/2011.09763/) (2020)
- [Quantifying Explainers of Graph Neural Networks in Computational Pathology](https://mlsanity.com/paper/2011.12646/) (2020)
- [CPP-Net: Context-aware Polygon Proposal Network for Nucleus Segmentation](https://mlsanity.com/paper/2102.06867/) (2021)
- [Relation DETR: Exploring Explicit Position Relation Prior for Object Detection](https://mlsanity.com/paper/2407.11699/) (2024)
- [Multi-Class Cell Detection Using Spatial Context Representation](https://mlsanity.com/paper/2110.04886/) (2021)
- [DoNet: Deep De-overlapping Network for Cytology Instance Segmentation](https://mlsanity.com/paper/2303.14373/) (2023)
- [Which Pixel to Annotate: a Label-Efficient Nuclei Segmentation Framework](https://mlsanity.com/paper/2212.10305/) (2022)
- [Structure Embedded Nucleus Classification for Histopathology Images](https://mlsanity.com/paper/2302.11416/) (2023)

## Abstract (arXiv)

Accurate cell detection and classification are crucial for pathological analysis, directly affecting diagnostic accuracy and treatment planning. To capture complex cellular interactions beyond visual appearance within the tumor microenvironment, several approaches have employed graph neural networks to model spatial and relational patterns among cell nuclei, yielding promising results. However, these methods typically adopt a two-stage paradigm of visual extraction followed by relational modeling, which necessitates separate tuning for each stage, thereby increasing pipeline complexity and hindering end-to-end joint optimization. In this paper, we propose an end-to-end framework for cell detection and classification that jointly models patch-level visual representations and instance-level interactions, which incorporates a dynamic graph construction module and an instance-aware graph network. Specifically, the graph construction module dynamically builds the graph structure using learnable queries derived from patch-level features as cell instance representations, with adjacency defined by integrating feature similarity and spatial distances. The instance-aware graph network performs adaptive instance filtering and feature reorganization, aggregating them over the cell graph into a topological latent state for a selective state-space transition driven by visual cues, fusing appearance and relational evidence. When evaluated on multiple datasets with different staining protocols for cell and nucleus detection, our method significantly outperforms existing approaches in both detection and classification performance. The code will be released at https://github.com/RuochenLiu23/IGM.