Yutong Sun

Shunxing Bao, Sichen Zhu, Vasantha L Kolachala et al.

Crohn's disease (CD) is a chronic and relapsing inflammatory condition that affects segments of the gastrointestinal tract. CD activity is determined by histological findings, particularly the density of neutrophils observed on Hematoxylin and Eosin stains (H&E) imaging. However, understanding the broader morphometry and local cell arrangement beyond cell counting and tissue morphology remains challenging. To address this, we characterize six distinct cell types from H&E images and develop a novel approach for the local spatial signature of each cell. Specifically, we create a 10-cell neighborhood matrix, representing neighboring cell arrangements for each individual cell. Utilizing t-SNE for non-linear spatial projection in scatter-plot and Kernel Density Estimation contour-plot formats, our study examines patterns of differences in the cellular environment associated with the odds ratio of spatial patterns between active CD and control groups. This analysis is based on data collected at the two research institutes. The findings reveal heterogeneous nearest-neighbor patterns, signifying distinct tendencies of cell clustering, with a particular focus on the rectum region. These variations underscore the impact of data heterogeneity on cell spatial arrangements in CD patients. Moreover, the spatial distribution disparities between the two research sites highlight the significance of collaborative efforts among healthcare organizations. All research analysis pipeline tools are available at https://github.com/MASILab/cellNN.

Stephen A. Goss, Robert J. Steininger, Dhruv Narayanan et al.

As artificial intelligence research advances, the platforms used to evaluate AI agents need to adapt and grow to continue to challenge them. We present the Polycraft World AI Lab (PAL), a task simulator with an API based on the Minecraft mod Polycraft World. Our platform is built to allow AI agents with different architectures to easily interact with the Minecraft world, train and be evaluated in multiple tasks. PAL enables the creation of tasks in a flexible manner as well as having the capability to manipulate any aspect of the task during an evaluation. All actions taken by AI agents and external actors (non-player-characters, NPCs) in the open-world environment are logged to streamline evaluation. Here we present two custom tasks on the PAL platform, one focused on multi-step planning and one focused on navigation, and evaluations of agents solving them. In summary, we report a versatile and extensible AI evaluation platform with a low barrier to entry for AI researchers to utilize.

Yutong Sun, Sichen Zhu, Peng Qiu

The rapid development of digital pathology and modern deep learning has facilitated the emergence of pathology foundation models that are expected to solve general pathology problems under various disease conditions in one unified model, with or without fine-tuning. In parallel, spatial transcriptomics has emerged as a transformative technology that enables the profiling of gene expression on hematoxylin and eosin (H&E) stained histology images. Spatial transcriptomics unlocks the unprecedented opportunity to dive into existing histology images at a more granular, cellular level. In this work, we propose a lightweight and training-efficient approach to predict cellular composition directly from H&E-stained histology images by leveraging information-enriched feature embeddings extracted from pre-trained pathology foundation models. By training a lightweight multi-layer perceptron (MLP) regressor on cell-type abundances derived via cell2location, our method efficiently distills knowledge from pathology foundation models and demonstrates the ability to accurately predict cell-type compositions from histology images, without physically performing the costly spatial transcriptomics. Our method demonstrates competitive performance compared to existing methods such as Hist2Cell, while significantly reducing computational complexity.

Yutong Sun, Mohit Prabhushankar, Ghassan AlRegib

In this paper, we show that existing recognition and localization deep architectures, that have not been exposed to eye tracking data or any saliency datasets, are capable of predicting the human visual saliency. We term this as implicit saliency in deep neural networks. We calculate this implicit saliency using expectancy-mismatch hypothesis in an unsupervised fashion. Our experiments show that extracting saliency in this fashion provides comparable performance when measured against the state-of-art supervised algorithms. Additionally, the robustness outperforms those algorithms when we add large noise to the input images. Also, we show that semantic features contribute more than low-level features for human visual saliency detection.