# Preserving Marker Specificity with Lightweight Channel-Independent Representation Learning

arXiv: https://arxiv.org/abs/2512.15410 · HTML: https://mlsanity.com/paper/2512.15410/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 31 references that are in the map.
- First posted on arXiv 17 Dec 2025.

## Builds on (most cited first, 10 of 10)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [VICReg: Variance-Invariance-Covariance Regularization for Self-Supervised Learning](https://mlsanity.com/paper/2105.04906/) (2021)
- [HyperDense-Net: A hyper-densely connected CNN for multi-modal image segmentation](https://mlsanity.com/paper/1804.02967/) (2018)
- [Software for Dataset-wide XAI: From Local Explanations to Global Insights with Zennit, CoRelAy, and ViRelAy](https://mlsanity.com/paper/2106.13200/) (2021)
- [A Closer Look at Multimodal Representation Collapse](https://mlsanity.com/paper/2505.22483/) (2025)
- [Pretrained ViTs Yield Versatile Representations For Medical Images](https://mlsanity.com/paper/2303.07034/) (2023)
- [A Foundation Model for Spatial Proteomics](https://mlsanity.com/paper/2506.03373/) (2025)
- [Let it shine: Autofluorescence of Papanicolaou-stain improves AI-based cytological oral cancer detection](https://mlsanity.com/paper/2407.01869/) (2024)

## Abstract (arXiv)

Multiplexed tissue imaging measures dozens of protein markers per cell, yet most deep learning models still apply early channel fusion, assuming shared structure across markers. We investigate whether preserving marker independence, combined with deliberately shallow architectures, provides a more suitable inductive bias for self-supervised representation learning in multiplex data than increasing model scale. Using a Hodgkin lymphoma CODEX dataset with 145,000 cells and 49 markers, we compare standard early-fusion CNNs with channel-separated architectures, including a marker-aware baseline and our novel shallow Channel-Independent Model (CIM-S) with 5.5K parameters. After contrastive pretraining and linear evaluation, early-fusion models show limited ability to retain marker-specific information and struggle particularly with rare-cell discrimination. Channel-independent architectures, and CIM-S in particular, achieve substantially stronger representations despite their compact size. These findings are consistent across multiple self-supervised frameworks, remain stable across augmentation settings, and are reproducible across both the 49-marker and reduced 18-marker settings. These results show that lightweight, channel-independent architectures can match or surpass deep early-fusion CNNs and foundation models for multiplex representation learning. Code is available at https://github.com/SimonBon/CIM-S.