Abstract Weakly supervised image segmentation is a challenging problem in computer vision fifield. In this paper, we present a new weakly supervised image segmentation algorithm by learning the distribution of spatially structured superpixel sets from image-level labels. Specififically, we fifirst extract graphlets from each image where a graphlet is a smallsized graph consisting of superpixels as its nodes and it encapsulates the spatial structure of those superpixels. Then, a manifold embedding algorithm is proposed to transform graphlets of different sizes into equal-length feature vectors. Thereafter, we use GMM to learn the distribution of the post-embedding graphlets. Finally, we propose a novel image segmentation algorithm, called graphlet cut, that leverages the learned graphlet distribution in measuring the homogeneity of a set of spatially structured superpixels. Experimental results show that the proposed approach outperforms state-of-the-art weakly supervised image segmentation methods, and its performance is comparable to those of the fully supervised segmentation models.