In pathology, accurate and efficient analysis of Hematoxylin and Eosin (H\&E) slides is crucial for timely and effective cancer diagnosis. Although many deep learning solutions for nuclei instance segmentation and classification exist in the literature, they often entail high computational costs and resource requirements, thus limiting their practical usage in medical applications. To address this issue, we introduce a novel convolutional neural network, NuLite, a U-Net-like architecture designed explicitly on Fast-ViT, a state-of-the-art (SOTA) lightweight CNN. We obtained three versions of our model, NuLite-S, NuLite-M, and NuLite-H, trained on the PanNuke dataset. The experimental results prove that our models equal CellViT (SOTA) in terms of panoptic quality and detection. However, our lightest model, NuLite-S, is 40 times smaller in terms of parameters and about 8 times smaller in terms of GFlops, while our heaviest model is 17 times smaller in terms of parameters and about 7 times smaller in terms of GFlops. Moreover, our model is up to about 8 times faster than CellViT. Lastly, to prove the effectiveness of our solution, we provide a robust comparison of external datasets, namely CoNseP, MoNuSeg, and GlySAC. Our model is publicly available at https://github.com/CosmoIknosLab/NuLite
This paper introduces a new technique to measure the feature dependency of neural network models. The motivation is to better understand a model by querying whether it is using information from human-understandable features, e.g., anatomical shape, volume, or image texture. Our method is based on the principle that if a model is dependent on a feature, then removal of that feature should significantly harm its performance. A targeted feature is "removed" by collapsing the dimension in the data distribution that corresponds to that feature. We perform this by moving data points along the feature dimension to a baseline feature value while staying on the data manifold, as estimated by a deep generative model. Then we observe how the model's performance changes on the modified test data set, with the target feature dimension removed. We test our method on deep neural network models trained on synthetic image data with known ground truth, an Alzheimer's disease prediction task using MRI and hippocampus segmentations from the OASIS-3 dataset, and a cell nuclei classification task using the Lizard dataset.
Nuclei classification is a critical step in computer-aided diagnosis with histopathology images. In the past, various methods have employed graph neural networks (GNN) to analyze cell graphs that model inter-cell relationships by considering nuclei as vertices. However, they are limited by the GNN mechanism that only passes messages among local nodes via fixed edges. To address the issue, we develop a cell graph transformer (CGT) that treats nodes and edges as input tokens to enable learnable adjacency and information exchange among all nodes. Nevertheless, training the transformer with a cell graph presents another challenge. Poorly initialized features can lead to noisy self-attention scores and inferior convergence, particularly when processing the cell graphs with numerous connections. Thus, we further propose a novel topology-aware pretraining method that leverages a graph convolutional network (GCN) to learn a feature extractor. The pre-trained features may suppress unreasonable correlations and hence ease the finetuning of CGT. Experimental results suggest that the proposed cell graph transformer with topology-aware pretraining significantly improves the nuclei classification results, and achieves the state-of-the-art performance. Code and models are available at https://github.com/lhaof/CGT