A Nuclei-Focused Strategy for Automated Histopathology Grading of Renal Cell Carcinoma

1Korea University, 2The Catholic University of Korea College of Medicine

Abstract

The rising incidence of kidney cancer underscores the need for precise and reproducible diagnostic methods. In particular, renal cell carcinoma (RCC), the most prevalent type of kidney cancer, requires accurate nuclear grading for better prognostic prediction. Recent advances in deep learning have facilitated end-to-end diagnostic methods using contextual features in histopathological images. However, most existing methods focus only on image-level features or lack an effective process for aggregating nuclei prediction results, limiting their diagnostic accuracy. In this paper, we introduce a novel framework, Nuclei feature Assisted Patch-level RCC grading (NuAP-RCC), that leverages nuclei-level features for enhanced patch-level RCC grading. Our approach employs a nuclei-level RCC grading network to extract grade-aware features, which serve as node features in a graph. These node features are aggregated using graph neural networks to capture the morphological characteristics and distributions of the nuclei. The aggregated features are then combined with global image-level features extracted by convolutional neural networks, resulting in a final feature for accurate RCC grading. In addition, we present a new dataset for patch-level RCC grading. Experimental results demonstrate the superior accuracy and generalizability of NuAP-RCC across datasets from different medical institutions, achieving a 6.15% improvement over the second best model in accuracy on our USM-RCC dataset.

USM-RCC

Check the link for downloading our USM-RCC dataset.

Visualization Results

Examples of the detected nuclei and the visualizations of the attention scores of the CNN feature and GNN feature.

Visualization of patch-level prediction on whole slide images.

visualization 3

Ablation study

We present the ablation study results to analyze the effectiveness of our hyperparameter settings, such as the number of epochs, the batch size, and the learning rate.


Epochs

The training loss GANFE is converged around at 50 epochs.

loss curve 1

The training loss GNNFA is converged around at 100 epochs.

loss curve 2


Batch size

The table below presents qualitative results for different batch sizes.

Batch size (GANFE) Precision Recall F1 Accuracy
2 0.7223 0.7130 0.7133 0.7130
4 0.7219 0.7150 0.7141 0.7150
8 0.7049 0.6980 0.7003 0.6980
Batch size (GNNFA) Precision Recall F1 Accuracy
8 0.7854 ± 0.0511 0.7630 ± 0.0604 0.7639 ± 0.0562 0.7903 ± 0.0479
16 0.8037 ± 0.0407 0.7818 ± 0.0436 0.7841 ± 0.0428 0.8014 ± 0.0382
32 0.7952 ± 0.0428 0.7691 ± 0.0516 0.7731 ± 0.0483 0.7966 ± 0.0484


Learning rate

The table below presents qualitative results for different learning rates.

Learning rate (GANFE) Precision Recall F1 Accuracy
5e-2 0.7087 0.6870 0.6921 0.6870
1e-3 0.7219 0.7150 0.7141 0.7150
5e-3 0.6917 0.6770 0.6750 0.6770
Learning rate (GNNFA) Precision Recall F1 Accuracy
1e-3 0.8100 ± 0.0393 0.7723 ± 0.0598 0.7705 ± 0.0560 0.7978 ± 0.0460
1e-4 0.8037 ± 0.0407 0.7818 ± 0.0436 0.7841 ± 0.0428 0.8014 ± 0.0382
1e-5 0.7837 ± 0.0523 0.7410 ± 0.0434 0.7457 ± 0.0482 0.7895 ± 0.0399