# PointFISH -- learning point cloud representations for RNA localization patterns

arXiv: https://arxiv.org/abs/2302.10923 · HTML: https://mlsanity.com/paper/2302.10923/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 46 references that are in the map.
- First posted on arXiv 21 Feb 2023.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Rethinking the Inception Architecture for Computer Vision](https://mlsanity.com/paper/1512.00567/) (2015)
- [PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation](https://mlsanity.com/paper/1612.00593/) (2016)
- [PointNet++: Deep Hierarchical Feature Learning on Point Sets in a Metric Space](https://mlsanity.com/paper/1706.02413/) (2017)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [Point Transformer](https://mlsanity.com/paper/2011.00931/) (2020)
- [KPConv: Flexible and Deformable Convolution for Point Clouds](https://mlsanity.com/paper/1904.08889/) (2019)
- [Bag of Tricks for Efficient Text Classification](https://mlsanity.com/paper/1607.01759/) (2016)
- [PointCNN: Convolution On X-Transformed Points](https://mlsanity.com/paper/1801.07791/) (2018)
- [PointConv: Deep Convolutional Networks on 3D Point Clouds](https://mlsanity.com/paper/1811.07246/) (2018)
- [Rethinking Network Design and Local Geometry in Point Cloud: A Simple Residual MLP Framework](https://mlsanity.com/paper/2202.07123/) (2022)

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

- [FISHing in Uncertainty: Synthetic Contrastive Learning for Genetic Aberration Detection](https://mlsanity.com/paper/2411.01025/) (2024)

## Abstract (arXiv)

Subcellular RNA localization is a critical mechanism for the spatial control of gene expression. Its mechanism and precise functional role is not yet very well understood. Single Molecule Fluorescence in Situ Hybridization (smFISH) images allow for the detection of individual RNA molecules with subcellular accuracy. In return, smFISH requires robust methods to quantify and classify RNA spatial distribution. Here, we present PointFISH, a novel computational approach for the recognition of RNA localization patterns. PointFISH is an attention-based network for computing continuous vector representations of RNA point clouds. Trained on simulations only, it can directly process extracted coordinates from experimental smFISH images. The resulting embedding allows scalable and flexible spatial transcriptomics analysis and matches performance of hand-crafted pipelines.