# Stabilizing In-Context Multi-Source Domain Adaptation for Biomedical Images Through Controls

arXiv: https://arxiv.org/abs/2604.20824 · HTML: https://mlsanity.com/paper/2604.20824/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 30 of its 61 references that are in the map.
- First posted on arXiv 22 Apr 2026.

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

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Unsupervised Domain Adaptation by Backpropagation](https://mlsanity.com/paper/1409.7495/) (2014)
- [Moment Matching for Multi-Source Domain Adaptation](https://mlsanity.com/paper/1812.01754/) (2018)
- [Continual Test-Time Domain Adaptation](https://mlsanity.com/paper/2203.13591/) (2022)
- [LeViT: a Vision Transformer in ConvNet's Clothing for Faster Inference](https://mlsanity.com/paper/2104.01136/) (2021)
- [Return of Frustratingly Easy Domain Adaptation](https://mlsanity.com/paper/1511.05547/) (2015)
- [Unsupervised Pixel-Level Domain Adaptation with Generative Adversarial Networks](https://mlsanity.com/paper/1612.05424/) (2016)
- [Revisiting Batch Normalization For Practical Domain Adaptation](https://mlsanity.com/paper/1603.04779/) (2016)
- [A Brief Review of Domain Adaptation](https://mlsanity.com/paper/2010.03978/) (2020)
- [Coupled Generative Adversarial Networks](https://mlsanity.com/paper/1606.07536/) (2016)
- [Style Injection in Diffusion: A Training-free Approach for Adapting Large-scale Diffusion Models for Style Transfer](https://mlsanity.com/paper/2312.09008/) (2023)
- [Central Moment Discrepancy (CMD) for Domain-Invariant Representation Learning](https://mlsanity.com/paper/1702.08811/) (2017)
- [Parameter-free Online Test-time Adaptation](https://mlsanity.com/paper/2201.05718/) (2022)
- [Adaptive Risk Minimization: Learning to Adapt to Domain Shift](https://mlsanity.com/paper/2007.02931/) (2020)
- [NOTE: Robust Continual Test-time Adaptation Against Temporal Correlation](https://mlsanity.com/paper/2208.05117/) (2022)
- [Unsupervised Cross-Domain Image Generation](https://mlsanity.com/paper/1611.02200/) (2016)
- [Entropy is not Enough for Test-Time Adaptation: From the Perspective of Disentangled Factors](https://mlsanity.com/paper/2403.07366/) (2024)
- [Universal Test-time Adaptation through Weight Ensembling, Diversity Weighting, and Prior Correction](https://mlsanity.com/paper/2306.00650/) (2023)
- [On Pitfalls of Test-Time Adaptation](https://mlsanity.com/paper/2306.03536/) (2023)
- [Multi-Source Domain Adaptation with Mixture of Experts](https://mlsanity.com/paper/1809.02256/) (2018)
- [Curriculum Manager for Source Selection in Multi-Source Domain Adaptation](https://mlsanity.com/paper/2007.01261/) (2020)
- [Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology](https://mlsanity.com/paper/2404.10242/) (2024)
- [RxRx1: A Dataset for Evaluating Experimental Batch Correction Methods](https://mlsanity.com/paper/2301.05768/) (2023)
- [Your Classifier can Secretly Suffice Multi-Source Domain Adaptation](https://mlsanity.com/paper/2103.11169/) (2021)
- [Domain Aggregation Networks for Multi-Source Domain Adaptation](https://mlsanity.com/paper/1909.05352/) (2019)
- [Label Shift Adapter for Test-Time Adaptation under Covariate and Label Shifts](https://mlsanity.com/paper/2308.08810/) (2023)
- [A Short Survey on Importance Weighting for Machine Learning](https://mlsanity.com/paper/2403.10175/) (2024)
- [Bridging Generalization Gaps in High Content Imaging Through Online Self-Supervised Domain Adaptation](https://mlsanity.com/paper/2311.12623/) (2023)

## Abstract (arXiv)

Biomedical imaging data presents enormous potential for deep learning models to predict invaluable properties, such as diseases and drug effects. However, unavoidable alterations of the technical conditions cause batch effects: variations between groups of samples that are not due to any biological signal of interest. Batch effects greatly hinder the generalization abilities of deep learning models, preventing their practical use in the real world. Unsupervised Domain Adaptation (UDA) methods have been proposed to mitigate batch effects, but they usually assume that the data is comprised of only one source domain and one target domain, whereas biological datasets are comprised of multiple domains, both at training and at inference time. While Batch Normalization-based test-time and meta-learning adaptation methods offer a promising mechanism for domain alignment, we show that existing approaches exhibit degraded performance under the usual inference scenarios of small target batch sizes and label shift. We address these limitations by leveraging negative control samples, which are consistently present in every experimental batch in biological datasets, as stable context for adaptation. We propose CS-ARM-BN, a meta-learning BN adaptation method that uses controls both during training and inference to stabilize domain statistics. We perform a suite of experiments of Mechanism-Of-Action (MoA) classification, a crucial task for drug discovery, on the large JUMP-CP imaging dataset. Our experiments show that CS-ARM-BN substantially improves robustness to batch size and class distribution shifts, enabling practical use of deep learning models for biomedical images.