SENCA-st: Integrating Spatial Transcriptomics and Histopathology with Cross Attention Shared Encoder for Region Identification in Cancer Pathology

Spatial transcriptomics is an emerging field that enables the identification of functional regions based on the spatial distribution of gene expression. Integrating this functional information present in transcriptomic data with structural data from histopathology images is an active research area with applications in identifying tumor substructures associated with cancer drug resistance. Current histopathology-spatial-transcriptomic region segmentation methods suffer due to either making spatial transcriptomics prominent by using histopathology features just to assist processing spatial transcriptomics data or using vanilla contrastive learning that make histopathology images prominent due to only promoting common features losing functional information. In both extremes, the model gets either lost in the noise of spatial transcriptomics or overly smoothed, losing essential information. Thus, we propose our novel architecture SENCA-st (Shared Encoder with Neighborhood Cross Attention) that preserves the features of both modalities. More importantly, it emphasizes regions that are structurally similar in histopathology but functionally different on spatial transcriptomics using cross-attention. We demonstrate the superior performance of our model that surpasses state-of-the-art methods in detecting tumor heterogeneity and tumor micro-environment regions, a clinically crucial aspect.

A-TPT: Angular Diversity Calibration Properties for Test-Time Prompt Tuning of Vision-Language Models

Test-time prompt tuning (TPT) has emerged as a promising technique for adapting large vision-language models (VLMs) to unseen tasks without relying on labeled data. However, the lack of dispersion between textual features can hurt calibration performance, which raises concerns about VLMs' reliability, trustworthiness, and safety. Current TPT approaches primarily focus on improving prompt calibration by either maximizing average textual feature dispersion or enforcing orthogonality constraints to encourage angular separation. However, these methods may not always have optimal angular separation between class-wise textual features, which implies overlooking the critical role of angular diversity. To address this, we propose A-TPT, a novel TPT framework that introduces angular diversity to encourage uniformity in the distribution of normalized textual features induced by corresponding learnable prompts. This uniformity is achieved by maximizing the minimum pairwise angular distance between features on the unit hypersphere. We show that our approach consistently surpasses state-of-the-art TPT methods in reducing the aggregate average calibration error while maintaining comparable accuracy through extensive experiments with various backbones on different datasets. Notably, our approach exhibits superior zero-shot calibration performance on natural distribution shifts and generalizes well to medical datasets. We provide extensive analyses, including theoretical aspects, to establish the grounding of A-TPT. These results highlight the potency of promoting angular diversity to achieve well-dispersed textual features, significantly improving VLM calibration during test-time adaptation. Our code will be made publicly available.

CrossVideoMAE: Self-Supervised Image-Video Representation Learning with Masked Autoencoders

Current video-based Masked Autoencoders (MAEs) primarily focus on learning effective spatiotemporal representations from a visual perspective, which may lead the model to prioritize general spatial-temporal patterns but often overlook nuanced semantic attributes like specific interactions or sequences that define actions - such as action-specific features that align more closely with human cognition for space-time correspondence. This can limit the model's ability to capture the essence of certain actions that are contextually rich and continuous. Humans are capable of mapping visual concepts, object view invariance, and semantic attributes available in static instances to comprehend natural dynamic scenes or videos. Existing MAEs for videos and static images rely on separate datasets for videos and images, which may lack the rich semantic attributes necessary for fully understanding the learned concepts, especially when compared to using video and corresponding sampled frame images together. To this end, we propose CrossVideoMAE an end-to-end self-supervised cross-modal contrastive learning MAE that effectively learns both video-level and frame-level rich spatiotemporal representations and semantic attributes. Our method integrates mutual spatiotemporal information from videos with spatial information from sampled frames within a feature-invariant space, while encouraging invariance to augmentations within the video domain. This objective is achieved through jointly embedding features of visible tokens and combining feature correspondence within and across modalities, which is critical for acquiring rich, label-free guiding signals from both video and frame image modalities in a self-supervised manner. Extensive experiments demonstrate that our approach surpasses previous state-of-the-art methods and ablation studies validate the effectiveness of our approach.