HistoKernel: Whole Slide Image Level Maximum Mean Discrepancy Kernels for Pan-Cancer Predictive Modelling
<|reference_start|>HistoKernel: Whole Slide Image Level Maximum Mean Discrepancy Kernels for Pan-Cancer Predictive Modelling: Machine learning in computational pathology (CPath) often aggregates patch-level predictions from multi-gigapixel Whole Slide Images (WSIs) to generate WSI-level prediction scores for crucial tasks such as survival prediction and drug effect prediction. However, current methods do not explicitly characterize distributional differences between patch sets within WSIs. We introduce HistoKernel, a novel Maximum Mean Discrepancy (MMD) kernel that measures distributional similarity between WSIs for enhanced prediction performance on downstream prediction tasks.   Our comprehensive analysis demonstrates HistoKernel's effectiveness across various machine learning tasks, including retrieval (n = 9,362), drug sensitivity regression (n = 551), point mutation classification (n = 3,419), and survival analysis (n = 2,291), outperforming existing deep learning methods. Additionally, HistoKernel seamlessly integrates multi-modal data and offers a novel perturbation-based method for patch-level explainability. This work pioneers the use of kernel-based methods for WSI-level predictive modeling, opening new avenues for research. Code is available at https://github.com/pkeller00/HistoKernel.<|reference_end|>
@article{keller2024histokernel:,
    title={HistoKernel: Whole Slide Image Level Maximum Mean Discrepancy Kernels
  for Pan-Cancer Predictive Modelling},
    author={Piotr Keller, Muhammad Dawood, Brinder Singh Chohan and Fayyaz ul Amir
  Afsar Minhas},
    journal={arXiv preprint arXiv:2408.05195},
    year={2024},
    archivePrefix={arXiv},
    eprint={2408.05195},
    primaryClass={cs.LG cs.AI}
}