# FISHing in Uncertainty: Synthetic Contrastive Learning for Genetic Aberration Detection

arXiv: https://arxiv.org/abs/2411.01025 · HTML: https://mlsanity.com/paper/2411.01025/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 31 references that are in the map.
- First posted on arXiv 1 Nov 2024.

## Builds on (most cited first, 13 of 13)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Mitigating Neural Network Overconfidence with Logit Normalization](https://mlsanity.com/paper/2205.09310/) (2022)
- [Deep Deterministic Uncertainty: A Simple Baseline](https://mlsanity.com/paper/2102.11582/) (2021)
- [Contrastive Training for Improved Out-of-Distribution Detection](https://mlsanity.com/paper/2007.05566/) (2020)
- [Image Classification with Deep Learning in the Presence of Noisy Labels: A Survey](https://mlsanity.com/paper/1912.05170/) (2019)
- [Probabilistic Contrastive Learning Recovers the Correct Aleatoric Uncertainty of Ambiguous Inputs](https://mlsanity.com/paper/2302.02865/) (2023)
- [A Simple Framework for Uncertainty in Contrastive Learning](https://mlsanity.com/paper/2010.02038/) (2020)
- [Uncertainty in Contrastive Learning: On the Predictability of Downstream Performance](https://mlsanity.com/paper/2207.09336/) (2022)
- [PointFISH -- learning point cloud representations for RNA localization patterns](https://mlsanity.com/paper/2302.10923/) (2023)

## Abstract (arXiv)

Detecting genetic aberrations is crucial in cancer diagnosis, typically through fluorescence in situ hybridization (FISH). However, existing FISH image classification methods face challenges due to signal variability, the need for costly manual annotations and fail to adequately address the intrinsic uncertainty. We introduce a novel approach that leverages synthetic images to eliminate the requirement for manual annotations and utilizes a joint contrastive and classification objective for training to account for inter-class variation effectively. We demonstrate the superior generalization capabilities and uncertainty calibration of our method, which is trained on synthetic data, by testing it on a manually annotated dataset of real-world FISH images. Our model offers superior calibration in terms of classification accuracy and uncertainty quantification with a classification accuracy of 96.7% among the 50% most certain cases. The presented end-to-end method reduces the demands on personnel and time and improves the diagnostic workflow due to its accuracy and adaptability. All code and data is publicly accessible at: https://github.com/SimonBon/FISHing