# Exploring the Interplay Between Colorectal Cancer Subtypes Genomic Variants and Cellular Morphology: A Deep-Learning Approach

arXiv: https://arxiv.org/abs/2303.14703 · HTML: https://mlsanity.com/paper/2303.14703/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 26 references that are in the map.
- First posted on arXiv 26 Mar 2023.

## Builds on (most cited first, 7 of 7)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Rethinking the Inception Architecture for Computer Vision](https://mlsanity.com/paper/1512.00567/) (2015)
- [Going Deeper with Convolutions](https://mlsanity.com/paper/1409.4842/) (2014)
- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [Interventional Bag Multi-Instance Learning On Whole-Slide Pathological Images](https://mlsanity.com/paper/2303.06873/) (2023)
- [DeepSMILE: Contrastive self-supervised pre-training benefits MSI and HRD classification directly from H&E whole-slide images in colorectal and breast cancer](https://mlsanity.com/paper/2107.09405/) (2021)

## Abstract (arXiv)

Molecular subtypes of colorectal cancer (CRC) significantly influence treatment decisions. While convolutional neural networks (CNNs) have recently been introduced for automated CRC subtype identification using H&E stained histopathological images, the correlation between CRC subtype genomic variants and their corresponding cellular morphology expressed by their imaging phenotypes is yet to be fully explored. The goal of this study was to determine such correlations by incorporating genomic variants in CNN models for CRC subtype classification from H&E images. We utilized the publicly available TCGA-CRC-DX dataset, which comprises whole slide images from 360 CRC-diagnosed patients (260 for training and 100 for testing). This dataset also provides information on CRC subtype classifications and genomic variations. We trained CNN models for CRC subtype classification that account for potential correlation between genomic variations within CRC subtypes and their corresponding cellular morphology patterns. We assessed the interplay between CRC subtypes' genomic variations and cellular morphology patterns by evaluating the CRC subtype classification accuracy of the different models in a stratified 5-fold cross-validation experimental setup using the area under the ROC curve (AUROC) and average precision (AP) as the performance metrics. Combining the CNN models account for variations in CIMP and SNP further improved classification accuracy (AUROC: 0.847±0.01 vs. 0.787±0.03, p=0.01, AP: 0.68±0.02 vs. 0.64±0.05).