用主动学习减少标注量,让生物医学图像分割更省力高效。
An Active Learning Pipeline for Biomedical Image Instance Segmentation with Minimal Human Intervention
- 先用大模型生成伪标签,再自动配置nnU-Net模型。
- 仅需少量人工标注核心数据集,即可实现高性能分割。
- 适合缺乏标注资源的生物医学研究者快速上手先进模型。
生物医学图像分割对结构精确定界和下游分析至关重要。传统方法易受噪声干扰,而U-Net等深度学习模型虽性能优异,但通常依赖大量标注数据。nnU-Net虽能自动配置模型,仍需充足标注用于交叉验证,当仅有原始图像无标签时难以应用。大模型具备零样本泛化能力,但在特定数据集上表现可能不足。本文提出一种以数据为中心的主动学习流程:先由大模型生成伪标签,用于nnU-Net的自配置;再从中选取代表性子集进行最小化人工标注,实现模型有效微调。该方法显著降低标注需求,同时保持领先性能,为生物医学研究者提供可快速部署的先进分割方案。代码已开源于https://github.com/MMV-Lab/AL_BioMed_img_seg。
原文摘要 · Abstract (English)
Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation performance. nnU-Net further automates model configuration, making it adaptable across datasets without extensive tuning. However, it requires a substantial amount of annotated data for cross-validation, posing a challenge when only raw images but no labels are available. Large foundation models offer zero-shot generalizability, but may underperform on specific datasets with unique characteristics, limiting their direct use for analysis. This work addresses these bottlenecks by proposing a data-centric AI workflow that leverages active learning and pseudo-labeling to combine the strengths of traditional neural networks and large foundation models while minimizing human intervention. The pipeline starts by generating pseudo-labels from a foundation model, which are then used for nnU-Net's self-configuration. Subsequently, a representative core-set is selected for minimal manual annotation, enabling effective fine-tuning of the nnU-Net model. This approach significantly reduces the need for manual annotations while maintaining competitive performance, providing an accessible solution for biomedical researchers to apply state-of-the-art AI techniques in their segmentation tasks. The code is available at https://github.com/MMV-Lab/AL_BioMed_img_seg.
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