In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative potential, the prohibitive cost of ST technology remains a significant barrier to its widespread adoption in large-scale studies. An alternative, more cost-effective strategy involves employing artificial intelligence to predict gene expression levels using readily accessible whole-slide images stained with Hematoxylin and Eosin (H&E). However, existing methods have yet to fully capitalize on multimodal information provided by H&E images and ST data with spatial location. In this paper, we propose mclSTExp, a multimodal contrastive learning with Transformer and Densenet-121 encoder for Spatial Transcriptomics Expression prediction. We conceptualize each spot as a “word”, integrating its intrinsic features with spatial context through the self-attention mechanism of a Transformer encoder. This integration is further enriched by incorporating image features via contrastive learning, thereby enhancing the predictive capability of our model. We conducted an extensive evaluation of highly variable genes in two breast cancer datasets and a skin squamous cell carcinoma dataset, and the results demonstrate that mclSTExp exhibits superior performance in predicting spatial gene expression. Moreover, mclSTExp has shown promise in interpreting cancer-specific overexpressed genes, elucidating immune-related genes, and identifying specialized spatial domains annotated by pathologists. Our source code is available at https://github.com/shizhiceng/mclSTExp.

Most facial landmark detection methods predict landmarks by mapping the input facial appearance features to landmark heatmaps and have achieved promising results. However, when the face image is suffering from large poses, heavy occlusions and complicated illuminations, they cannot learn discriminative feature representations and effective facial shape constraints, nor can they accurately predict the value of each element in the landmark heatmap, limiting their detection accuracy. To address this problem, we propose a novel Reference Heatmap Transformer (RHT) by introducing reference heatmap information for more precise facial landmark detection. The proposed RHT consists of a Soft Transformation Module (STM) and a Hard Transformation Module (HTM), which can cooperate with each other to encourage the accurate transformation of the reference heatmap information and facial shape constraints. Then, a Multi-Scale Feature Fusion Module (MSFFM) is proposed to fuse the transformed heatmap features and the semantic features learned from the original face images to enhance feature representations for producing more accurate target heatmaps. To the best of our knowledge, this is the first study to explore how to enhance facial landmark detection by transforming the reference heatmap information. The experimental results from challenging benchmark datasets demonstrate that our proposed method outperforms the state-of-the-art methods in the literature.

Heatmap regression (HR) has become one of the mainstream approaches for face alignment and has obtained promising results under constrained environments. However, when a face image suffers from large pose variations, heavy occlusions and complicated illuminations, the performances of HR methods degrade greatly due to the low resolutions of the generated landmark heatmaps and the exclusion of important high-order information that can be used to learn more discriminative features. To address the alignment problem for faces with extremely large poses and heavy occlusions, this paper proposes a heatmap subpixel regression (HSR) method and a multi-order cross geometry-aware (MCG) model, which are seamlessly integrated into a novel multi-order high-precision hourglass network (MHHN). The HSR method is proposed to achieve high-precision landmark detection by a well-designed subpixel detection loss (SDL) and subpixel detection technology (SDT). At the same time, the MCG model is able to use the proposed multi-order cross information to learn more discriminative representations for enhancing facial geometric constraints and context information. To the best of our knowledge, this is the first study to explore heatmap subpixel regression for robust and high-precision face alignment. The experimental results from challenging benchmark datasets demonstrate that our approach outperforms state-of-the-art methods in the literature.

Recently, heatmap regression has been widely explored in facial landmark detection and obtained remarkable performance. However, most of the existing heatmap regression-based facial landmark detection methods neglect to explore the high-order feature correlations, which is very important to learn more representative features and enhance shape constraints. Moreover, no explicit global shape constraints have been added to the final predicted landmarks, which leads to a reduction in accuracy. To address these issues, in this article, we propose a multiorder multiconstraint deep network (MMDN) for more powerful feature correlations and shape constraints’ learning. Especially, an implicit multiorder correlating geometry-aware (IMCG) model is proposed to introduce the multiorder spatial correlations and multiorder channel correlations for more discriminative representations. Furthermore, an explicit probability-based boundary-adaptive regression (EPBR) method is developed to enhance the global shape constraints and further search the semantically consistent landmarks in the predicted boundary for robust facial landmark detection. It is interesting to show that the proposed MMDN can generate more accurate boundary-adaptive landmark heatmaps and effectively enhance shape constraints to the predicted landmarks for faces with large pose variations and heavy occlusions. Experimental results on challenging benchmark data sets demonstrate the superiority of our MMDN over state-of-the-art facial landmark detection methods.