Must: Maximizing Latent Capacity of Spatial Transcriptomics Data

Spatial transcriptomics (ST) technologies have revolutionized the study of gene expression patterns in tissues by providing multimodality data in transcriptomic, spatial, and morphological, offering opportunities for understanding tissue biology beyond transcriptomics. However, we identify the modality bias phenomenon in ST data species, i.e., the inconsistent contribution of different modalities to the labels leads to a tendency for the analysis methods to retain the information of the dominant modality. How to mitigate the adverse effects of modality bias to satisfy various downstream tasks remains a fundamental challenge. This paper introduces Multiple-modality Structure Transformation, named MuST, a novel methodology to tackle the challenge. MuST integrates the multi-modality information contained in the ST data effectively into a uniform latent space to provide a foundation for all the downstream tasks. It learns intrinsic local structures by topology discovery strategy and topology fusion loss function to solve the inconsistencies among different modalities. Thus, these topology-based and deep learning techniques provide a solid foundation for a variety of analytical tasks while coordinating different modalities. The effectiveness of MuST is assessed by performance metrics and biological significance. The results show that it outperforms existing state-of-the-art methods with clear advantages in the precision of identifying and preserving structures of tissues and biomarkers. MuST offers a versatile toolkit for the intricate analysis of complex biological systems.

Video Captioning in Compressed Video

Existing approaches in video captioning concentrate on exploring global frame features in the uncompressed videos, while the free of charge and critical saliency information already encoded in the compressed videos is generally neglected. We propose a video captioning method which operates directly on the stored compressed videos. To learn a discriminative visual representation for video captioning, we design a residuals-assisted encoder (RAE), which spots regions of interest in I-frames under the assistance of the residuals frames. First, we obtain the spatial attention weights by extracting features of residuals as the saliency value of each location in I-frame and design a spatial attention module to refine the attention weights. We further propose a temporal gate module to determine how much the attended features contribute to the caption generation, which enables the model to resist the disturbance of some noisy signals in the compressed videos. Finally, Long Short-Term Memory is utilized to decode the visual representations into descriptions. We evaluate our method on two benchmark datasets and demonstrate the effectiveness of our approach.