The rapid development of spatial transcriptomics allows the measurement of RNA abundance at a high spatial resolution, making it possible to simultaneously profile gene expression, spatial locations of cells or spots, and the corresponding hematoxylin and eosin-stained histology images. It turns promising to predict gene expression from histology images that are relatively easy and cheap to obtain. For this purpose, several methods are devised, but they have not fully captured the internal relations of the 2D vision features or spatial dependency between spots. Here, we developed Hist2ST, a deep learning-based model to predict RNA-seq expression from histology images. Around each sequenced spot, the corresponding histology image is cropped into an image patch and fed into a convolutional module to extract 2D vision features. Meanwhile, the spatial relations with the whole image and neighbored patches are captured through Transformer and graph neural network modules, respectively. These learned features are then used to predict the gene expression by following the zero-inflated negative binomial distribution. To alleviate the impact by the small spatial transcriptomics data, a self-distillation mechanism is employed for efficient learning of the model. By comprehensive tests on cancer and normal datasets, Hist2ST was shown to outperform existing methods in terms of both gene expression prediction and spatial region identification. Further pathway analyses indicated that our model could reserve biological information. Thus, Hist2ST enables generating spatial transcriptomics data from histology images for elucidating molecular signatures of tissues.

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Detecting dense landmarks for diverse clothes, as a fundamental technique for clothes analysis, has attracted increasing research attention due to its huge application potential. However, due to the lack of modeling underlying semantic layout constraints among landmarks, prior works often detect ambiguous and structure-inconsistent landmarks of multiple overlapped clothes in one person. In this paper, we propose to seamlessly enforce structural layout relationships among landmarks on the intermediate representations via multiple stacked layout-graph reasoning layers. We define the layout-graph as a hierarchical structure including a root node, body-part nodes (e.g. upper body, lower body), coarse clothes-part nodes (e.g. collar, sleeve) and leaf landmark nodes (e.g. left-collar, rightcollar). Each Layout-Graph Reasoning(LGR) layer aims to map feature representations into structural graph nodes via a Map-to-Node module, performs reasoning over structural graph nodes to achieve global layout coherency via a layout-graph reasoning module, and then maps graph nodes back to enhance feature representations via a Nodeto-Map module. The layout-graph reasoning module integrates a graph clustering operation to generate representations of intermediate nodes (bottom-up inference) and then a graph deconvolution operation (top-down inference) over the whole graph. Extensive experiments on two public fashion landmark datasets demonstrate the superiority of our model. Furthermore, to advance the fine-grained fashion landmark research for supporting more comprehensive clothes generation and attribute recognition, we contribute the first Fine-grained Fashion Landmark Dataset (FFLD) containing 200k images annotated with at most 32 keypoints for 13 clothes types.

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