Rethinking model prototyping through the MedMNIST+ dataset collection

Abstract

The integration of deep learning based systems in clinical practice is often impeded by challenges rooted in limited and heterogeneous medical datasets. In addition, the field has increasingly prioritized marginal performance gains on a few, narrowly scoped benchmarks over clinical applicability, slowing down meaningful algorithmic progress. This trend often results in excessive fine-tuning of existing methods on selected datasets rather than fostering clinically relevant innovations. In response, this work introduces a comprehensive benchmark for the MedMNIST+ dataset collection, designed to diversify the evaluation landscape across several imaging modalities, anatomical regions, classification tasks and sample sizes. We systematically reassess commonly used Convolutional Neural Networks (CNNs) and Vision Transformer (ViT) architectures across distinct medical datasets, training methodologies, and input resolutions to validate and refine existing assumptions about model effectiveness and development. Our findings suggest that computationally efficient training schemes and modern foundation models offer viable alternatives to costly end-to-end training. Additionally, we observe that higher image resolutions do not consistently improve performance beyond a certain threshold. This highlights the potential benefits of using lower resolutions, particularly in prototyping stages, to reduce computational demands without sacrificing accuracy. Notably, our analysis reaffirms the competitiveness of CNNs compared to ViTs, emphasizing the importance of comprehending the intrinsic capabilities of different architectures. Finally, by establishing a standardized evaluation framework, we aim to enhance transparency, reproducibility, and comparability within the MedMNIST+ dataset collection as well as future research. Code is available at (https://github.com/sdoerrich97/rethinking-model-prototyping-MedMNISTPlus).

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