# FATE: Feature-Agnostic Transformer-based Encoder for learning generalized embedding spaces in flow cytometry data

arXiv: https://arxiv.org/abs/2311.03314 · HTML: https://mlsanity.com/paper/2311.03314/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 42 references that are in the map.
- First posted on arXiv 6 Nov 2023.

## Builds on (most cited first, 18 of 18)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [ConvNeXt V2: Co-designing and Scaling ConvNets with Masked Autoencoders](https://mlsanity.com/paper/2301.00808/) (2023)
- [Masked Autoencoders As Spatiotemporal Learners](https://mlsanity.com/paper/2205.09113/) (2022)
- [Point-M2AE: Multi-scale Masked Autoencoders for Hierarchical Point Cloud Pre-training](https://mlsanity.com/paper/2205.14401/) (2022)
- [Dream3D: Zero-Shot Text-to-3D Synthesis Using 3D Shape Prior and Text-to-Image Diffusion Models](https://mlsanity.com/paper/2212.14704/) (2022)
- [Contrastive Audio-Visual Masked Autoencoder](https://mlsanity.com/paper/2210.07839/) (2022)
- [GraphMAE2: A Decoding-Enhanced Masked Self-Supervised Graph Learner](https://mlsanity.com/paper/2304.04779/) (2023)
- [MAE-AST: Masked Autoencoding Audio Spectrogram Transformer](https://mlsanity.com/paper/2203.16691/) (2022)
- [CLIP-GEN: Language-Free Training of a Text-to-Image Generator with CLIP](https://mlsanity.com/paper/2203.00386/) (2022)
- [MAELi: Masked Autoencoder for Large-Scale LiDAR Point Clouds](https://mlsanity.com/paper/2212.07207/) (2022)
- [Self-supervised Pre-training with Masked Shape Prediction for 3D Scene Understanding](https://mlsanity.com/paper/2305.05026/) (2023)
- [Automated Identification of Cell Populations in Flow Cytometry Data with Transformers](https://mlsanity.com/paper/2108.10072/) (2021)

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

- [Automated Immunophenotyping Assessment for Diagnosing Childhood Acute Leukemia using Set-Transformers](https://mlsanity.com/paper/2406.18309/) (2024)
- [On the importance of local and global feature learning for automated measurable residual disease detection in flow cytometry data](https://mlsanity.com/paper/2411.15621/) (2024)

## Abstract (arXiv)

While model architectures and training strategies have become more generic and flexible with respect to different data modalities over the past years, a persistent limitation lies in the assumption of fixed quantities and arrangements of input features. This limitation becomes particularly relevant in scenarios where the attributes captured during data acquisition vary across different samples. In this work, we aim at effectively leveraging data with varying features, without the need to constrain the input space to the intersection of potential feature sets or to expand it to their union. We propose a novel architecture that can directly process data without the necessity of aligned feature modalities by learning a general embedding space that captures the relationship between features across data samples with varying sets of features. This is achieved via a set-transformer architecture augmented by feature-encoder layers, thereby enabling the learning of a shared latent feature space from data originating from heterogeneous feature spaces. The advantages of the model are demonstrated for automatic cancer cell detection in acute myeloid leukemia in flow cytometry data, where the features measured during acquisition often vary between samples. Our proposed architecture's capacity to operate seamlessly across incongruent feature spaces is particularly relevant in this context, where data scarcity arises from the low prevalence of the disease. The code is available for research purposes at https://github.com/lisaweijler/FATE.