Teaching pathology foundation models to accurately predict gene expression with parameter efficient knowledge transfer

Gene expression profiling provides critical insights into cellular heterogeneity, biological processes and disease mechanisms. There has been an increasing interest in computational approaches that can predict gene expression directly from digitalized histopathology images. While image foundation models have shown promise in a variety of pathology downstream analysis, their performances on gene-expression prediction are still limited. Explicitly incorporating information from the transcriptomic models can help image models to address domain shift, yet the fine-tuning and alignment of foundation models can be expensive. In the work, we propose Parameter Efficient Knowledge trAnsfer (PEKA), a novel framework that leverages Block-Affine Adaptation and integrates knowledge distillation and structure alignment losses for cross-modal knowledge transfer. We evaluated PEKA for gene expression prediction using multiple spatial transcriptomics datasets (comprising 206,123 image tiles with matched gene expression profiles) that encompassed various types of tissue. PEKA achieved at least 5\% performance improvement over baseline foundation models while also outperforming alternative parameter-efficient fine-tuning strategies. We will release the code, datasets and aligned models after peer-review to facilitate broader adoption and further development for parameter efficient model alignment.

ImViD: Immersive Volumetric Videos for Enhanced VR Engagement

User engagement is greatly enhanced by fully immersive multi-modal experiences that combine visual and auditory stimuli. Consequently, the next frontier in VR/AR technologies lies in immersive volumetric videos with complete scene capture, large 6-DoF interaction space, multi-modal feedback, and high resolution & frame-rate contents. To stimulate the reconstruction of immersive volumetric videos, we introduce ImViD, a multi-view, multi-modal dataset featuring complete space-oriented data capture and various indoor/outdoor scenarios. Our capture rig supports multi-view video-audio capture while on the move, a capability absent in existing datasets, significantly enhancing the completeness, flexibility, and efficiency of data capture. The captured multi-view videos (with synchronized audios) are in 5K resolution at 60FPS, lasting from 1-5 minutes, and include rich foreground-background elements, and complex dynamics. We benchmark existing methods using our dataset and establish a base pipeline for constructing immersive volumetric videos from multi-view audiovisual inputs for 6-DoF multi-modal immersive VR experiences. The benchmark and the reconstruction and interaction results demonstrate the effectiveness of our dataset and baseline method, which we believe will stimulate future research on immersive volumetric video production.

Den-SOFT: Dense Space-Oriented Light Field DataseT for 6-DOF Immersive Experience

We have built a custom mobile multi-camera large-space dense light field capture system, which provides a series of high-quality and sufficiently dense light field images for various scenarios. Our aim is to contribute to the development of popular 3D scene reconstruction algorithms such as IBRnet, NeRF, and 3D Gaussian splitting. More importantly, the collected dataset, which is much denser than existing datasets, may also inspire space-oriented light field reconstruction, which is potentially different from object-centric 3D reconstruction, for immersive VR/AR experiences. We utilized a total of 40 GoPro 10 cameras, capturing images of 5k resolution. The number of photos captured for each scene is no less than 1000, and the average density (view number within a unit sphere) is 134.68. It is also worth noting that our system is capable of efficiently capturing large outdoor scenes. Addressing the current lack of large-space and dense light field datasets, we made efforts to include elements such as sky, reflections, lights and shadows that are of interest to researchers in the field of 3D reconstruction during the data capture process. Finally, we validated the effectiveness of our provided dataset on three popular algorithms and also integrated the reconstructed 3DGS results into the Unity engine, demonstrating the potential of utilizing our datasets to enhance the realism of virtual reality (VR) and create feasible interactive spaces. The dataset is available at our project website.