# Automated HER2 scoring with uncertainty quantification using lensfree holography and deep learning

arXiv: https://arxiv.org/abs/2601.18219 · HTML: https://mlsanity.com/paper/2601.18219/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 52 references that are in the map.
- First posted on arXiv 26 Jan 2026.

## Builds on (most cited first, 22 of 22)

- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Neural Architecture Search with Reinforcement Learning](https://mlsanity.com/paper/1611.01578/) (2016)
- [All-Optical Machine Learning Using Diffractive Deep Neural Networks](https://mlsanity.com/paper/1804.08711/) (2018)
- [Deep Learning-enabled Virtual Histological Staining of Biological Samples](https://mlsanity.com/paper/2211.06822/) (2022)
- [PhaseStain: Digital staining of label-free quantitative phase microscopy images using deep learning](https://mlsanity.com/paper/1807.07701/) (2018)
- [Design of Task-Specific Optical Systems Using Broadband Diffractive Neural Networks](https://mlsanity.com/paper/1909.06553/) (2019)
- [Label-free virtual HER2 immunohistochemical staining of breast tissue using deep learning](https://mlsanity.com/paper/2112.05240/) (2021)
- [Ensemble learning of diffractive optical networks](https://mlsanity.com/paper/2009.06869/) (2020)
- [Fourier Imager Network (FIN): A deep neural network for hologram reconstruction with superior external generalization](https://mlsanity.com/paper/2204.10533/) (2022)
- [Class-specific Differential Detection in Diffractive Optical Neural Networks Improves Inference Accuracy](https://mlsanity.com/paper/1906.03417/) (2019)
- [Super-resolution image display using diffractive decoders](https://mlsanity.com/paper/2206.07281/) (2022)
- [Unidirectional Imaging using Deep Learning-Designed Materials](https://mlsanity.com/paper/2212.02025/) (2022)
- [eFIN: Enhanced Fourier Imager Network for generalizable autofocusing and pixel super-resolution in holographic imaging](https://mlsanity.com/paper/2301.03162/) (2023)
- [All-Optical Phase Conjugation Using Diffractive Wavefront Processing](https://mlsanity.com/paper/2311.04473/) (2023)
- [Pixel super-resolved virtual staining of label-free tissue using diffusion models](https://mlsanity.com/paper/2410.20073/) (2024)
- [Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning](https://mlsanity.com/paper/2207.00089/) (2022)
- [All-optical image classification through unknown random diffusers using a single-pixel diffractive network](https://mlsanity.com/paper/2208.03968/) (2022)
- [Neural Network-Based Processing and Reconstruction of Compromised Biophotonic Image Data](https://mlsanity.com/paper/2403.14324/) (2024)
- [Automated HER2 Scoring in Breast Cancer Images Using Deep Learning and Pyramid Sampling](https://mlsanity.com/paper/2404.00837/) (2024)
- [BlurryScope enables compact, cost-effective scanning microscopy for HER2 scoring using deep learning on blurry images](https://mlsanity.com/paper/2410.17557/) (2024)
- [Autonomous Uncertainty Quantification for Computational Point-of-care Sensors](https://mlsanity.com/paper/2512.21335/) (2025)

## Abstract (arXiv)

Accurate assessment of human epidermal growth factor receptor 2 (HER2) expression is critical for breast cancer diagnosis, prognosis, and therapy selection; yet, most existing digital HER2 scoring methods rely on bulky and expensive optical systems. Here, we present a compact and cost-effective lensfree holography platform integrated with deep learning for automated HER2 scoring of immunohistochemically stained breast tissue sections. The system captures lensfree diffraction patterns of stained HER2 tissue sections under RGB laser illumination and acquires complex field information over a sample area of ~1,250 mm^2 at an effective throughput of ~84 mm^2 per minute. To enhance diagnostic reliability, we incorporated an uncertainty quantification strategy based on Bayesian Monte Carlo dropout, which provides autonomous uncertainty estimates for each prediction and supports reliable, robust HER2 scoring, with an overall correction rate of 30.4%. Using a blinded test set of 412 unique tissue samples, our approach achieved a testing accuracy of 84.9% for 4-class (0, 1+, 2+, 3+) HER2 classification and 94.8% for binary (0/1+ vs. 2+/3+) HER2 scoring with uncertainty quantification. Overall, this lensfree holography approach provides a practical pathway toward portable, high-throughput, and cost-effective HER2 scoring, particularly suited for resource-limited settings, where traditional digital pathology infrastructure is unavailable.