Effect of Patch Size on Fine-Tuning Vision Transformers in Two-Dimensional and Three-Dimensional Medical Image Classification

Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a predefined size and necessitating pre-processing steps like resizing, padding, or cropping. This poses challenges in medical imaging, particularly with irregularly shaped structures like tumors. A fixed bounding box crop size produces input images with highly variable foreground-to-background ratios. Resizing medical images can degrade information and introduce artefacts, impacting diagnosis. Hence, tailoring variable-sized crops to regions of interest can enhance feature representation capabilities. Moreover, large images are computationally expensive, and smaller sizes risk information loss, presenting a computation-accuracy tradeoff. We propose VariViT, an improved ViT model crafted to handle variable image sizes while maintaining a consistent patch size. VariViT employs a novel positional embedding resizing scheme for a variable number of patches. We also implement a new batching strategy within VariViT to reduce computational complexity, resulting in faster training and inference times. In our evaluations on two 3D brain MRI datasets, VariViT surpasses vanilla ViTs and ResNet in glioma genotype prediction and brain tumor classification. It achieves F1-scores of 75.5% and 76.3%, respectively, learning more discriminative features. Our proposed batching strategy reduces computation time by up to 30% compared to conventional architectures. These findings underscore the efficacy of VariViT in image representation learning. Our code can be found here: https://github.com/Aswathi-Varma/varivit

Vision Transformers rely on positional embeddings and class tokens encoding fixed spatial priors. While effective for natural images, these priors may be suboptimal when spatial layout is weakly informative, a frequent condition in medical imaging. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a compact Vision Transformer that removes positional embeddings and the [CLS] token, achieving permutation-invariant patch processing via global average pooling. Zero-token denotes removal of the dedicated aggregation token and positional encodings. Patch tokens remain unchanged. Adaptive residual projections preserve training stability under strict parameter constraints. We evaluate ZACH-ViT across seven MedMNIST datasets under a strict few-shot protocol (50 samples/class, fixed hyperparameters, five seeds). Results reveal regime-dependent behavior: ZACH-ViT (0.25M parameters, trained from scratch) achieves strongest advantage on BloodMNIST and remains competitive on PathMNIST, while relative advantage decreases on datasets with stronger anatomical priors (OCTMNIST, OrganAMNIST), consistent with our hypothesis. Component and pooling ablations show positional support becomes mildly beneficial as spatial structure increases, whereas reintroducing a [CLS] token is consistently unfavorable. These findings support that architectural alignment with data structure can outweigh universal benchmark dominance. Despite minimal size and no pretraining, ZACH-ViT achieves competitive performance under data-scarce conditions, relevant for compact medical imaging and low-resource settings. Code: https://github.com/Bluesman79/ZACH-ViT

Vision Transformer (ViT) has brought new breakthroughs to the field of image classification by introducing the self-attention mechanism and Graph Convolutional Networks(GCN) have been proposed and successfully applied in data representation and analysis. However, there are key challenges which limit their further development: (1) The patch size selected by ViT is crucial for accurate predictions, which raises a natural question: How to select the size of patches properly or how to comprehensively combine small patches and larger patches; (2) While the spatial structure information is important in vision tasks, the 1D position embeddings fails to capture the spatial structure information of patches more accurately; (3) The GCN can capture the local connectivity relationships between image nodes, but it lacks the ability to capture global graph structural information. On the contrary, the self-attention mechanism of ViT can draw the global relation on image patches, but it is unable to model the local structure of image. To overcome such limitations, we propose the Hierarchical Vision Transformer Enhanced by Graph Convolutional Network (GCN-HViT) for image classification. Specifically, the Hierarchical ViT we designed can model patch-wise information interactions on a global scale within each level and model hierarchical relationships between small patches and large patches across multiple levels. In addition, the proposed GCN method functions as a local feature extractor to obtain the local representation of each image patch which serves as a 2D position embedding of each patch in the 2D space. Meanwhile, it models patch-wise information interactions on a local scale within each level. Extensive experiments on 3 real-world datasets demonstrate that GCN-HViT achieves state-of-the-art performance.