# Using Deep Learning Models Pretrained by Self-Supervised Learning for Protein Localization

arXiv: https://arxiv.org/abs/2604.10970 · HTML: https://mlsanity.com/paper/2604.10970/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 47 references that are in the map.
- First posted on arXiv 13 Apr 2026.

## Builds on (most cited first, 14 of 14)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [ImageNet Large Scale Visual Recognition Challenge](https://mlsanity.com/paper/1409.0575/) (2014)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Channel Vision Transformers: An Image Is Worth 1 x 16 x 16 Words](https://mlsanity.com/paper/2309.16108/) (2023)
- [CHAMMI: A benchmark for channel-adaptive models in microscopy imaging](https://mlsanity.com/paper/2310.19224/) (2023)
- [Weakly Supervised Set-Consistency Learning Improves Morphological Profiling of Single-Cell Images](https://mlsanity.com/paper/2406.05308/) (2024)
- [ChA-MAEViT: Unifying Channel-Aware Masked Autoencoders and Multi-Channel Vision Transformers for Improved Cross-Channel Learning](https://mlsanity.com/paper/2503.19331/) (2025)
- [CHAMMI-75: Pre-training multi-channel models with heterogeneous microscopy images](https://mlsanity.com/paper/2512.20833/) (2025)
- [Generalization of Self-Supervised Vision Transformers for Protein Localization Across Microscopy Domains](https://mlsanity.com/paper/2602.05527/) (2026)

## Abstract (arXiv)

Background: Task-specific microscopy datasets are often small, making it difficult to train deep learning models that learn robust features. While self-supervised learning (SSL) has shown promise through pretraining on large, domain-specific datasets, generalizability across datasets with differing staining protocols and channel configurations remains underexplored. We investigated the generalizability of SSL models pretrained on ImageNet-1k and HPA FOV, evaluating their embeddings on OpenCell with and without fine-tuning, two channel-mismatch strategies, and varying fine-tuning data fractions. We additionally analyzed single-cell embeddings on a labeled OpenCell subset. Result: DINO-based ViT backbones pretrained on HPA FOV or ImageNet-1k transfer well to OpenCell even without fine-tuning. Fine-tuning further improved performance to 0.704 ± 0.027 (17 classes, multi-class labels). At the single-cell level, the HPA single-cell-pretrained model achieved the highest k-nearest neighbor performance across all neighborhood sizes (macro F1 ≥ 0.515). Conclusion: SSL methods like DINO, pretrained on large domain-relevant datasets, enable effective use of deep learning features for fine-tuning on small, task-specific microscopy datasets.