3D medical image segmentation is a challenging task with crucial implications for disease diagnosis and treatment planning. Recent advances in deep learning have significantly enhanced fully supervised medical image segmentation. However, this approach heavily relies on labor-intensive and time-consuming fully annotated ground-truth labels, particularly for 3D volumes. To overcome this limitation, we propose a novel probabilistic-aware weakly supervised learning pipeline, specifically designed for 3D medical imaging. Our pipeline integrates three innovative components: a Probability-based Pseudo-Label Generation technique for synthesizing dense segmentation masks from sparse annotations, a Probabilistic Multi-head Self-Attention network for robust feature extraction within our Probabilistic Transformer Network, and a Probability-informed Segmentation Loss Function to enhance training with annotation confidence. Demonstrating significant advances, our approach not only rivals the performance of fully supervised methods but also surpasses existing weakly supervised methods in CT and MRI datasets, achieving up to 18.1% improvement in Dice scores for certain organs. The code is available at https://github.com/runminjiang/PW4MedSeg .

Subtomogram alignment is a critical task in cryo-electron tomography (cryo-ET) analysis, essential for achieving high-resolution reconstructions of macromolecular complexes. However, learning effective positional representations remains challenging due to limited labels and high noise levels inherent in cryo-ET data. In this work, we address this challenge by proposing a self-supervised learning approach that leverages intrinsic geometric transformations as implicit supervisory signals, enabling robust representation learning despite data scarcity. We introduce BOE-ViT, the first Vision Transformer (ViT) framework for 3D subtomogram alignment. Recognizing that traditional ViTs lack equivariance and are therefore suboptimal for orientation estimation, we enhance the model with two innovative modules that introduce equivariance include 1) the Polyshift module for improved shift estimation and 2) Multi-Axis Rotation Encoding (MARE) for enhanced rotation estimation. Experimental results demonstrate that BOE-ViT significantly outperforms state-of-the-art methods. Notably, at SNR 0.01 dataset, our approach achieves a 77.3% reduction in rotation estimation error and a 62.5% reduction in translation estimation error, effectively overcoming the challenges in cryo-ET subtomogram alignment.