Alexander Zhou

Zelong Liu, Andrew Tieu, Nikhil Patel et al.

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present VIsualization and Segmentation Masked AutoEncoder (VIS-MAE), novel model weights specifically designed for medical imaging. Specifically, VIS-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET,X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VIS-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications. In addition, VIS-MAE has improved label efficiency as it can achieve similar performance to other models with a reduced amount of labeled training data (50% or 80%) compared to other pre-trained weights. VIS-MAE represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload. The source code of this work is available at https://github.com/lzl199704/VIS-MAE.

Alexander Zhou, Zelong Liu, Andrew Tieu et al.

In this retrospective study, we annotated 44 structures on two datasets: an internal dataset of 1,518 MRI sequences from 843 patients at the Mount Sinai Health System, and an external dataset of 397 MRI sequences from 263 patients for benchmarking. The internal dataset trained the nnU-Net model MRAnnotator, which demonstrated strong generalizability on the external dataset. MRAnnotator outperformed existing models such as TotalSegmentator MRI and MRSegmentator on both datasets, achieving an overall average Dice score of 0.878 on the internal dataset and 0.875 on the external set. Model weights are available on GitHub, and the external test set can be shared upon request.

Yufan Zheng, Wei Jiang, Alexander Zhou et al.

Among various spatio-temporal prediction tasks, epidemic forecasting plays a critical role in public health management. Recent studies have demonstrated the strong potential of spatio-temporal graph neural networks (STGNNs) in extracting heterogeneous spatio-temporal patterns for epidemic forecasting. However, most of these methods bear an over-simplified assumption that two locations (e.g., cities) with similar observed features in previous time steps will develop similar infection numbers in the future. In fact, for any epidemic disease, there exists strong heterogeneity of its intrinsic evolution mechanisms across geolocation and time, which can eventually lead to diverged infection numbers in two ``similar'' locations. However, such mechanistic heterogeneity is non-trivial to be captured due to the existence of numerous influencing factors like medical resource accessibility, virus mutations, mobility patterns, etc., most of which are spatio-temporal yet unreachable or even unobservable. To address this challenge, we propose a Heterogeneous Epidemic-Aware Transmission Graph Neural Network (HeatGNN), a novel epidemic forecasting framework. By binding the epidemiology mechanistic model into a GNN, HeatGNN learns epidemiology-informed location embeddings of different locations that reflect their own transmission mechanisms over time. With the time-varying mechanistic affinity graphs computed with the epidemiology-informed location embeddings, a heterogeneous transmission graph network is designed to encode the mechanistic heterogeneity among locations, providing additional predictive signals to facilitate accurate forecasting. Experiments on three benchmark datasets have revealed that HeatGNN outperforms various strong baselines. Moreover, our efficiency analysis verifies the real-world practicality of HeatGNN on datasets of different sizes.

Haoyang Li, Yuming Xu, Chen Jason Zhang et al.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a $k$-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Zelong Liu, Alexander Zhou, Arnold Yang et al.

Deep learning in medical imaging often requires large-scale, high-quality data or initiation with suitably pre-trained weights. However, medical datasets are limited by data availability, domain-specific knowledge, and privacy concerns, and the creation of large and diverse radiologic databases like RadImageNet is highly resource-intensive. To address these limitations, we introduce RadImageGAN, the first multi-modal radiologic data generator, which was developed by training StyleGAN-XL on the real RadImageNet dataset of 102,774 patients. RadImageGAN can generate high-resolution synthetic medical imaging datasets across 12 anatomical regions and 130 pathological classes in 3 modalities. Furthermore, we demonstrate that RadImageGAN generators can be utilized with BigDatasetGAN to generate multi-class pixel-wise annotated paired synthetic images and masks for diverse downstream segmentation tasks with minimal manual annotation. We showed that using synthetic auto-labeled data from RadImageGAN can significantly improve performance on four diverse downstream segmentation datasets by augmenting real training data and/or developing pre-trained weights for fine-tuning. This shows that RadImageGAN combined with BigDatasetGAN can improve model performance and address data scarcity while reducing the resources needed for annotations for segmentation tasks.