# Segmentation and Risk Score Prediction of Head and Neck Cancers in PET/CT Volumes with 3D U-Net and Cox Proportional Hazard Neural Networks

arXiv: https://arxiv.org/abs/2202.07823 · HTML: https://mlsanity.com/paper/2202.07823/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 23 references that are in the map.
- First posted on arXiv 16 Feb 2022.

## Builds on (most cited first, 13 of 13)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation](https://mlsanity.com/paper/1809.10486/) (2018)
- [Time-to-Event Prediction with Neural Networks and Cox Regression](https://mlsanity.com/paper/1907.00825/) (2019)
- [Unified Focal loss: Generalising Dice and cross entropy-based losses to handle class imbalanced medical image segmentation](https://mlsanity.com/paper/2102.04525/) (2021)
- [Combo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation](https://mlsanity.com/paper/1805.02798/) (2018)
- [Recalibrating Fully Convolutional Networks with Spatial and Channel 'Squeeze & Excitation' Blocks](https://mlsanity.com/paper/1808.08127/) (2018)
- [AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy](https://mlsanity.com/paper/1808.05238/) (2018)
- [Mumford-Shah Loss Functional for Image Segmentation with Deep Learning](https://mlsanity.com/paper/1904.02872/) (2019)
- [Overview of the HECKTOR Challenge at MICCAI 2021: Automatic Head and Neck Tumor Segmentation and Outcome Prediction in PET/CT Images](https://mlsanity.com/paper/2201.04138/) (2022)
- [Squeeze-and-Excitation Normalization for Automated Delineation of Head and Neck Primary Tumors in Combined PET and CT Images](https://mlsanity.com/paper/2102.10446/) (2021)
- [Accurate Esophageal Gross Tumor Volume Segmentation in PET/CT using Two-Stream Chained 3D Deep Network Fusion](https://mlsanity.com/paper/1909.01524/) (2019)

## Built on by (most cited first, 2 of 2)

- [SwinCross: Cross-modal Swin Transformer for Head-and-Neck Tumor Segmentation in PET/CT Images](https://mlsanity.com/paper/2302.03861/) (2023)
- [Thyroidiomics: An Automated Pipeline for Segmentation and Classification of Thyroid Pathologies from Scintigraphy Images](https://mlsanity.com/paper/2407.10336/) (2024)

## Abstract (arXiv)

We utilized a 3D nnU-Net model with residual layers supplemented by squeeze and excitation (SE) normalization for tumor segmentation from PET/CT images provided by the Head and Neck Tumor segmentation chal-lenge (HECKTOR). Our proposed loss function incorporates the Unified Fo-cal and Mumford-Shah losses to take the advantage of distribution, region, and boundary-based loss functions. The results of leave-one-out-center-cross-validation performed on different centers showed a segmentation performance of 0.82 average Dice score (DSC) and 3.16 median Hausdorff Distance (HD), and our results on the test set achieved 0.77 DSC and 3.01 HD. Following lesion segmentation, we proposed training a case-control proportional hazard Cox model with an MLP neural net backbone to predict the hazard risk score for each discrete lesion. This hazard risk prediction model (CoxCC) was to be trained on a number of PET/CT radiomic features extracted from the segmented lesions, patient and lesion demographics, and encoder features provided from the penultimate layer of a multi-input 2D PET/CT convolutional neural network tasked with predicting time-to-event for each lesion. A 10-fold cross-validated CoxCC model resulted in a c-index validation score of 0.89, and a c-index score of 0.61 on the HECKTOR challenge test dataset.