As quantum chemical properties have a dependence on their geometries, graph neural networks (GNNs) using 3D geometric information have achieved high prediction accuracy in many tasks.

Many of the proposed GNN models with provable cycle counting power are based on subgraph GNNs, i.e., extracting a bag of subgraphs from

The success of graph neural networks (GNNs) largely relies on the process of aggregating information from neighbors defined by the input graph structures. Notably, message passing based GNNs, e.g., graph convolutional networks, leverage the immediate neighbors of each node during the aggregation process, and recently, graph diffusion convolution (GDC) is proposed to expand the propagation neighborhood by leveraging generalized graph diffusion. However, the neighborhood size in GDC is manually tuned for each graph by conducting grid search over the validation set, making its generalization practically limited. To address this issue, we propose the adaptive diffusion convolution (ADC) strategy to automatically learn the optimal neighborhood size from the data. Furthermore, we break the conventional assumption that all GNN layers and feature channels (dimensions) should use the same neighborhood for propagation. We design strategies to enable ADC to learn a dedicated propagation neighborhood for each GNN layer and each feature channel, making the GNN architecture fully coupled with graph structures---the unique property that differs GNNs from traditional neural networks. By directly plugging ADC into existing GNNs, we observe consistent and significant outperformance over both GDC and their vanilla versions across various datasets, demonstrating the improved model capacity brought by automatically learning unique neighborhood size per layer and per channel in GNNs.

As quantum chemical properties have a dependence on their geometries, graph neural networks (GNNs) using 3D geometric information have achieved high prediction accuracy in many tasks.

Many of the proposed GNN models with provable cycle counting power are based on subgraph GNNs, i.e., extracting a bag of subgraphs from

Processing-In-Memory (PIM) architectures offer a promising approach to accelerate Graph Neural Network (GNN) training and inference. However, various PIM devices such as ReRAM, FeFET, PCM, MRAM, and SRAM exist, with each device offering unique trade-offs in terms of power, latency, area, and non-idealities. A heterogeneous manycore architecture enabled by 3D integration can combine multiple PIM devices on a single platform, to enable energy-efficient and high-performance GNN training. In this work, we propose a 3D heterogeneous PIM-based accelerator for GNN training referred to as HePGA. We leverage the unique characteristics of GNN layers and associated computing kernels to optimize their mapping on to different PIM devices as well as planar tiers. Our experimental analysis shows that HePGA outperforms existing PIM-based architectures by up to 3.8x and 6.8x in energy-efficiency (TOPS/W) and compute efficiency (TOPS/mm2) respectively, without sacrificing the GNN prediction accuracy. Finally, we demonstrate the applicability of HePGA to accelerate inferencing of emerging transformer models.

Molecular representation learning, a cornerstone for downstream tasks like molecular captioning and molecular property prediction, heavily relies on Graph Neural Networks (GNN). However, GNN suffers from the over-smoothing problem, where node-level features collapse in deep GNN layers. While existing feature projection methods with cross-attention have been introduced to mitigate this issue, they still perform poorly in deep features. This motivated our exploration of using Mamba as an alternative projector for its ability to handle complex sequences. However, we observe that while Mamba excels at preserving global topological information from deep layers, it neglects fine-grained details in shallow layers. The capabilities of Mamba and cross-attention exhibit a global-local trade-off. To resolve this critical global-local trade-off, we propose Hierarchical and Structure-Aware Network (HSA-Net), a novel framework with two modules that enables a hierarchical feature projection and fusion. Firstly, a Hierarchical Adaptive Projector (HAP) module is introduced to process features from different graph layers. It learns to dynamically switch between a cross-attention projector for shallow layers and a structure-aware Graph-Mamba projector for deep layers, producing high-quality, multi-level features. Secondly, to adaptively merge these multi-level features, we design a Source-Aware Fusion (SAF) module, which flexibly selects fusion experts based on the characteristics of the aggregation features, ensuring a precise and effective final representation fusion. Extensive experiments demonstrate that our HSA-Net framework quantitatively and qualitatively outperforms current state-of-the-art (SOTA) methods.

In recent years, graph neural networks (GNN) have achieved unprecedented successes in node classification tasks. Although GNNs inherently encode specific inductive biases (e.g., acting as low-pass or high-pass filters), most existing methods implicitly assume conditional independence among node labels in their optimization objectives. While this assumption is suitable for traditional classification tasks such as image recognition, it contradicts the intuitive observation that node labels in graphs remain correlated, even after conditioning on the graph structure. To make structured predictions for node labels, we propose ReDiSC, namely, Reparameterized masked Diffusion model for Structured node Classification. ReDiSC estimates the joint distribution of node labels using a reparameterized masked diffusion model, which is learned through the variational expectation-maximization (EM) framework. Our theoretical analysis shows the efficiency advantage of ReDiSC in the E-step compared to DPM-SNC, a state-of-the-art model that relies on a manifold-constrained diffusion model in continuous domain. Meanwhile, we explicitly link ReDiSC's M-step objective to popular GNN and label propagation hybrid approaches. Extensive experiments demonstrate that ReDiSC achieves superior or highly competitive performance compared to state-of-the-art GNN, label propagation, and diffusion-based baselines across both homophilic and heterophilic graphs of varying sizes. Notably, ReDiSC scales effectively to large-scale datasets on which previous structured diffusion methods fail due to computational constraints, highlighting its significant practical advantage in structured node classification tasks.