# Metadata-guided Consistency Learning for High Content Images

arXiv: https://arxiv.org/abs/2212.11595 · HTML: https://mlsanity.com/paper/2212.11595/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 11 of its 32 references that are in the map.
- First posted on arXiv 22 Dec 2022.

## Builds on (most cited first, 11 of 11)

- [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)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [What Makes Transfer Learning Work For Medical Images: Feature Reuse & Other Factors](https://mlsanity.com/paper/2203.01825/) (2022)
- [Is it Time to Replace CNNs with Transformers for Medical Images?](https://mlsanity.com/paper/2108.09038/) (2021)
- [Contrastive Learning of Single-Cell Phenotypic Representations for Treatment Classification](https://mlsanity.com/paper/2103.16670/) (2021)

## Built on by (most cited first, 8 of 8)

- [Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology](https://mlsanity.com/paper/2404.10242/) (2024)
- [Masked Autoencoders are Scalable Learners of Cellular Morphology](https://mlsanity.com/paper/2309.16064/) (2023)
- [Weakly Supervised Set-Consistency Learning Improves Morphological Profiling of Single-Cell Images](https://mlsanity.com/paper/2406.05308/) (2024)
- [CLEF: Clinically-Guided Contrastive Learning for Electrocardiogram Foundation Models](https://mlsanity.com/paper/2512.02180/) (2025)
- [Bridging Generalization Gaps in High Content Imaging Through Online Self-Supervised Domain Adaptation](https://mlsanity.com/paper/2311.12623/) (2023)
- [Deep Learning for BioImaging: What Are We Really Learning?](https://mlsanity.com/paper/2603.13377/) (2026)
- [Who Needs Labels? Adapting Vision Foundation Models With the Metadata You Already Have](https://mlsanity.com/paper/2606.05107/) (2026)
- [HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy](https://mlsanity.com/paper/2607.04353/) (2026)

## Abstract (arXiv)

High content imaging assays can capture rich phenotypic response data for large sets of compound treatments, aiding in the characterization and discovery of novel drugs. However, extracting representative features from high content images that can capture subtle nuances in phenotypes remains challenging. The lack of high-quality labels makes it difficult to achieve satisfactory results with supervised deep learning. Self-Supervised learning methods have shown great success on natural images, and offer an attractive alternative also to microscopy images. However, we find that self-supervised learning techniques underperform on high content imaging assays. One challenge is the undesirable domain shifts present in the data known as batch effects, which are caused by biological noise or uncontrolled experimental conditions. To this end, we introduce Cross-Domain Consistency Learning (CDCL), a self-supervised approach that is able to learn in the presence of batch effects. CDCL enforces the learning of biological similarities while disregarding undesirable batch-specific signals, leading to more useful and versatile representations. These features are organised according to their morphological changes and are more useful for downstream tasks -- such as distinguishing treatments and mechanism of action.