HVTSurv: Hierarchical Vision Transformer for Patient-Level Survival
  Prediction from Whole Slide Image
Zhuchen Shao Yang Chen Hao Bian Jian Zhang Guojun Liu Yongbing Zhang
Survival prediction based on whole slide images (WSIs) is a challenging task
for patient-level multiple instance learning (MIL). Due to the vast amount of
data for a patient (one or multiple gigapixels WSIs) and the irregularly shaped
property of WSI, it is difficult to fully explore spatial, contextual, and
hierarchical interaction in the patient-level bag. Many studies adopt random
sampling pre-processing strategy and WSI-level aggregation models, which
inevitably lose critical prognostic information in the patient-level bag. In
this work, we propose a hierarchical vision Transformer framework named
HVTSurv, which can encode the local-level relative spatial information,
strengthen WSI-level context-aware communication, and establish patient-level
hierarchical interaction. Firstly, we design a feature pre-processing strategy,
including feature rearrangement and random window masking. Then, we devise
three layers to progressively obtain patient-level representation, including a
local-level interaction layer adopting Manhattan distance, a WSI-level
interaction layer employing spatial shuffle, and a patient-level interaction
layer using attention pooling. Moreover, the design of hierarchical network
helps the model become more computationally efficient. Finally, we validate
HVTSurv with 3,104 patients and 3,752 WSIs across 6 cancer types from The
Cancer Genome Atlas (TCGA). The average C-Index is 2.50-11.30% higher than all
the prior weakly supervised methods over 6 TCGA datasets. Ablation study and
attention visualization further verify the superiority of the proposed HVTSurv.
Implementation is available at: https://github.com/szc19990412/HVTSurv.