Hao Wu

Ammar Hoori, Sadeer Al-Kindi, Tao Hu et al.

Background. Coronary artery calcium (CAC) is a powerful predictor of major adverse cardiovascular events (MACE). Traditional Agatston score simply sums the calcium, albeit in a non-linear way, leaving room for improved calcification assessments that will more fully capture the extent of disease. Objective. To determine if AI methods using detailed calcification features (i.e., calcium-omics) can improve MACE prediction. Methods. We investigated additional features of calcification including assessment of mass, volume, density, spatial distribution, territory, etc. We used a Cox model with elastic-net regularization on 2457 CT calcium score (CTCS) enriched for MACE events obtained from a large no-cost CLARIFY program (ClinicalTri-als.gov Identifier: NCT04075162). We employed sampling techniques to enhance model training. We also investigated Cox models with selected features to identify explainable high-risk characteristics. Results. Our proposed calcium-omics model with modified synthetic down sampling and up sampling gave C-index (80.5%/71.6%) and two-year AUC (82.4%/74.8%) for (80:20, training/testing), respectively (sampling was applied to the training set only). Results compared favorably to Agatston which gave C-index (71.3%/70.3%) and AUC (71.8%/68.8%), respectively. Among calcium-omics features, numbers of calcifications, LAD mass, and diffusivity (a measure of spatial distribution) were important determinants of increased risk, with dense calcification (>1000HU) associated with lower risk. The calcium-omics model reclassified 63% of MACE patients to the high risk group in a held-out test. The categorical net-reclassification index was NRI=0.153. Conclusions. AI analysis of coronary calcification can lead to improved results as compared to Agatston scoring. Our findings suggest the utility of calcium-omics in improved prediction of risk.

Dongqi Fu, Zhigang Hua, Yan Xie et al.

Graph transformer has been proven as an effective graph learning method for its adoption of attention mechanism that is capable of capturing expressive representations from complex topological and feature information of graphs. Graph transformer conventionally performs dense attention (or global attention) for every pair of nodes to learn node representation vectors, resulting in quadratic computational costs that are unaffordable for large-scale graph data. Therefore, mini-batch training for graph transformers is a promising direction, but limited samples in each mini-batch can not support effective dense attention to encode informative representations. Facing this bottleneck, (1) we start by assigning each node a token list that is sampled by personalized PageRank (PPR) and then apply standard multi-head self-attention only on this list to compute its node representations. This PPR tokenization method decouples model training from complex graph topological information and makes heavy feature engineering offline and independent, such that mini-batch training of graph transformers is possible by loading each node's token list in batches. We further prove this PPR tokenization is viable as a graph convolution network with a fixed polynomial filter and jumping knowledge. However, only using personalized PageRank may limit information carried by a token list, which could not support different graph inductive biases for model training. To this end, (2) we rewire graphs by introducing multiple types of virtual connections through structure- and content-based super nodes that enable PPR tokenization to encode local and global contexts, long-range interaction, and heterophilous information into each node's token list, and then formalize our Virtual Connection Ranking based Graph Transformer (VCR-Graphormer).

Limei Wang, Kaveh Hassani, Si Zhang et al.

Transformers serve as the backbone architectures of Foundational Models, where domain-specific tokenizers allow them to adapt to various domains. Graph Transformers (GTs) have recently emerged as leading models in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities. To address this, we introduce GQT (\textbf{G}raph \textbf{Q}uantized \textbf{T}okenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 20 out of 22 benchmarks, including large-scale homophilic and heterophilic datasets.