Related papers: MINT: Molecularly Informed Training with Spatial T…
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with…
Spatial transcriptomics (ST) maps gene expression within tissue at individual spots, making it a valuable resource for multimodal representation learning. Additionally, ST inherently contains rich hierarchical information both across and…
Spatial transcriptomics reveals gene expression patterns within tissue context, enabling precision oncology applications such as treatment response prediction, but its high cost and technical complexity limit clinical adoption. Predicting…
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…
Masked image modeling (MIM) pre-training for large-scale vision transformers (ViTs) has enabled promising downstream performance on top of the learned self-supervised ViT features. In this paper, we question if the \textit{extremely simple}…
Spatial Transcriptomics (ST) reveals the spatial distribution of gene expression in tissues, offering critical insights into biological processes and disease mechanisms. However, the high cost, limited coverage, and technical complexity of…
Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell…
Whole slide imaging is fundamental to biomedical microscopy and computational pathology. Previously, learning representations for gigapixel-sized whole slide images (WSIs) has relied on multiple instance learning with weak labels, which do…
Multimodal self-supervised pretraining offers a promising route to cancer prognosis by integrating histopathology whole-slide images, gene expression, and pathology reports, yet most existing approaches require fully paired and complete…
Spatial Transcriptomics (ST) enables the measurement of gene expression while preserving spatial information, offering critical insights into tissue architecture and disease pathology. Recent developments have explored the use of…
While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer…
Recent self-supervised learning (SSL) methods have shown impressive results in learning visual representations from unlabeled images. This paper aims to improve their performance further by utilizing the architectural advantages of the…
Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised…
Masked image modeling (MIM) as pre-training is shown to be effective for numerous vision downstream tasks, but how and where MIM works remain unclear. In this paper, we compare MIM with the long-dominant supervised pre-trained models from…
Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can…
Self-supervised learning (SSL) has produced a diverse landscape of vision transformers (ViTs) whose pretrained representations support a wide range of downstream tasks. Towards a better understanding of these models, a body of work has…
While spatial transcriptomics (ST) has advanced our understanding of gene expression in tissue context, its high experimental cost limits its large-scale application. Predicting ST from pathology images is a promising, cost-effective…
Machine learning has achieved impressive performance in tomographic reconstruction, but supervised training requires paired measurements and ground-truth images that are often unavailable. This has motivated self-supervised approaches,…
Whole genome prediction of complex phenotypic traits using high-density genotyping arrays has attracted a great deal of attention, as it is relevant to the fields of plant and animal breeding and genetic epidemiology. As the number of…
Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic…