# FlowCyt: A Comparative Study of Deep Learning Approaches for Multi-Class Classification in Flow Cytometry Benchmarking

arXiv: https://arxiv.org/abs/2403.00024 · HTML: https://mlsanity.com/paper/2403.00024/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 4 of its 34 references that are in the map.
- First posted on arXiv 28 Feb 2024.

## Builds on (most cited first, 4 of 4)

- [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)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)

## Built on by (most cited first, 2 of 2)

- [Massive Activations in Graph Neural Networks: Decoding Attention for Domain-Dependent Interpretability](https://mlsanity.com/paper/2409.03463/) (2024)
- [Injecting Hierarchical Biological Priors into Graph Neural Networks for Flow Cytometry Prediction](https://mlsanity.com/paper/2405.18507/) (2024)

## Abstract (arXiv)

This paper presents FlowCyt, the first comprehensive benchmark for multi-class single-cell classification in flow cytometry data. The dataset comprises bone marrow samples from 30 patients, with each cell characterized by twelve markers. Ground truth labels identify five hematological cell types: T lymphocytes, B lymphocytes, Monocytes, Mast cells, and Hematopoietic Stem/Progenitor Cells (HSPCs). Experiments utilize supervised inductive learning and semi-supervised transductive learning on up to 1 million cells per patient. Baseline methods include Gaussian Mixture Models, XGBoost, Random Forests, Deep Neural Networks, and Graph Neural Networks (GNNs). GNNs demonstrate superior performance by exploiting spatial relationships in graph-encoded data. The benchmark allows standardized evaluation of clinically relevant classification tasks, along with exploratory analyses to gain insights into hematological cell phenotypes. This represents the first public flow cytometry benchmark with a richly annotated, heterogeneous dataset. It will empower the development and rigorous assessment of novel methodologies for single-cell analysis.