# An End-to-End Deep Learning Histochemical Scoring System for Breast Cancer Tissue Microarray

arXiv: https://arxiv.org/abs/1801.06288 · HTML: https://mlsanity.com/paper/1801.06288/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 19 Jan 2018.

## Built on by (most cited first, 4 of 4)

- [Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions](https://mlsanity.com/paper/2304.06662/) (2023)
- [A Discrete Scheme for Computing Image's Weighted Gaussian Curvature](https://mlsanity.com/paper/2101.07927/) (2021)
- [Deep Learning based Prediction of MSI using MMR Markers in Colorectal Cancer](https://mlsanity.com/paper/2203.00449/) (2022)
- [Preparing data for pathological artificial intelligence with clinical-grade performance](https://mlsanity.com/paper/2205.10748/) (2022)

## Abstract (arXiv)

One of the methods for stratifying different molecular classes of breast cancer is the Nottingham Prognostic Index Plus (NPI+) which uses breast cancer relevant biomarkers to stain tumour tissues prepared on tissue microarray (TMA). To determine the molecular class of the tumour, pathologists will have to manually mark the nuclei activity biomarkers through a microscope and use a semi-quantitative assessment method to assign a histochemical score (H-Score) to each TMA core. Manually marking positively stained nuclei is a time consuming, imprecise and subjective process which will lead to inter-observer and intra-observer discrepancies. In this paper, we present an end-to-end deep learning system which directly predicts the H-Score automatically. Our system imitates the pathologists' decision process and uses one fully convolutional network (FCN) to extract all nuclei region (tumour and non-tumour), a second FCN to extract tumour nuclei region, and a multi-column convolutional neural network which takes the outputs of the first two FCNs and the stain intensity description image as input and acts as the high-level decision making mechanism to directly output the H-Score of the input TMA image. To the best of our knowledge, this is the first end-to-end system that takes a TMA image as input and directly outputs a clinical score. We will present experimental results which demonstrate that the H-Scores predicted by our model have very high and statistically significant correlation with experienced pathologists' scores and that the H-Score discrepancy between our algorithm and the pathologists is on par with the inter-subject discrepancy between the pathologists.