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survival-deepmts's Introduction

DeepMTS: Deep Multi-Task Survival model for joint survival prediction and tumor segmentation

In this study, we propose a 3D end-to-end Deep Multi-Task Survival model (DeepMTS) for joint survival prediction and tumor segmentation. Our novelty is the introduction of a hard-sharing segmentation backbone to guide the extraction of local features related to the primary tumors, which reduces the interference from non-relevant background information. In addition, we also introduce a cascaded survival network to capture the prognostic information existing out of primary tumors and further leverage the global tumor information (e.g., tumor size, shape, and locations) derived from the segmentation backbone. Our experiments demonstrate that our DeepMTS can consistently outperform traditional radiomics-based survival models and existing deep survival models.
For more details, please refer to our paper. [IEEE] [arXiv]

Overview

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Publication

If this repository helps your work, please kindly cite our papers:

  • Mingyuan Meng, Bingxin Gu, Lei Bi, Shaoli Song, David Dagan Feng, Jinman Kim, "DeepMTS: Deep Multi-task Learning for Survival Prediction in Patients with Advanced Nasopharyngeal Carcinoma using Pretreatment PET/CT," IEEE Journal of Biomedical and Health Informatics, vol. 26, no. 9, pp. 4497-4507, 2022, doi: 10.1109/JBHI.2022.3181791. [IEEE] [arXiv]
  • Mingyuan Meng, Lei Bi, Dagan Feng, Jinman Kim, "Radiomics-enhanced Deep Multi-task Learning for Outcome Prediction in Head and Neck Cancer," Head and Neck Tumor Segmentation and Outcome Prediction (HECKTOR 2022), pp. 135-143, 2022, doi: 10.1007/978-3-031-27420-6_14. [Springer] [arXiv]
    (Ranked 2nd in HECKTOR2022 challenge, with only 0.00068 lower in C-index)

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survival-deepmts's Issues

The version of Tensorflow and Keras

Hi Mingyuan,

Thanks for your nice work and I am trying to follow it. I am wondering which version of Tensorflow and Keras did you use?

Best regards,
Yao

Request for Dataset Structure, Format, and Shape Details for Survival-DeepMTS Model

Hello,

I am highly interested in your project, Survival-DeepMTS, and I am eager to experiment with it. However, I noticed that the repository does not provide detailed information about the dataset structure, format, and shape required for the model.

Could you please provide the following details?

Dataset Structure: How is the dataset organized? Are there specific directories or files that need to be present, and how are they named or structured?
Data Format: What is the format of the data files? For example, are they in CSV, JSON, or another format?
Data Shape: What is the expected shape of the input data for the model? For instance, if the input is a 2D array, what are the dimensions?
Understanding these details would greatly help in preparing the dataset correctly for the model.

Thank you for your time and assistance!

Feature map visualization

Hi there! I really enjoyed reading your paper, very nice and interesting experiments that you did!
I just have a question regarding Figure S2 in your supplementary material, where you show feature map visualizations of Sur-HS, Sur-CasNet, MT-HS, MT-CasNet, and DeepMTS.
Which layer of your models was used to produce those feature maps? Or was an approach like Grad-CAM used for the creation of those heatmaps? Could you maybe also share the code to create those?
Thanks for providing some clues here!

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