Sampling methods (e.g., node-wise, layer-wise, or subgraph) has become an indispensable strategy to speed up training large-scale Graph Neural Networks (GNNs). However, existing sampling methods are mostly based on the graph structural information and ignore the dynamicity of optimization, which leads to high variance in estimating the stochastic gradients. The high variance issue can be very pronounced in extremely large graphs, where it results in slow convergence and poor generalization. In this paper, we theoretically analyze the variance of sampling methods and show that, due to the composite structure of empirical risk, the variance of any sampling method can be decomposed into embedding approximation variance in the forward stage and stochastic gradient variance in the backward stage that necessities mitigating both types of variance to obtain faster convergence rate. We propose a decoupled variance reduction strategy that employs (approximate) gradient information to adaptively sample nodes with minimal variance, and explicitly reduces the variance introduced by embedding approximation. We show theoretically and empirically that the proposed method, even with smaller mini-batch sizes, enjoys a faster convergence rate and entails a better generalization compared to the existing methods. CCS CONCEPTS• Computing methodologies → Machine learning; Learning latent representations.

Modern day drug discovery is extremely expensive and time consuming. Although computational approaches help accelerate and decrease the cost of drug discovery, existing computational software packages for docking-based drug discovery suffer from both low accuracy and high latency. A few recent machine learning-based approaches have been proposed for virtual screening by improving the ability to evaluate protein−ligand binding affinity, but such methods rely heavily on conventional docking software to sample docking poses, which results in excessive execution latencies. Here, we propose and evaluate a novel graph neural network (GNN)-based framework, MedusaGraph, which includes both pose-prediction (sampling) and pose-selection (scoring) models. Unlike the previous machine learning-centric studies, MedusaGraph generates the docking poses directly and achieves from 10 to 100 times speedup compared to state-of-the-art approaches, while having a slightly better docking accuracy.

Recurrent neural network (RNN) and self-attention mechanism (SAM) are the de facto methods to extract spatial-temporal information for temporal graph learning. Interestingly, we found that although both RNN and SAM could lead to a good performance, in practice neither of them is always necessary. In this paper, we propose GraphMixer, a conceptually and technically simple architecture that consists of three components: 1 a link-encoder that is only based on multi-layer perceptrons (MLP) to summarize the information from temporal links, 2 a node-encoder that is only based on neighbor mean-pooling to summarize node information, and 3 an MLP-based link classifier that performs link prediction based on the outputs of the encoders. Despite its simplicity, GraphMixer attains an outstanding performance on temporal link prediction benchmarks with faster convergence and better generalization performance. These results motivate us to rethink the importance of simpler model architecture. [Code].

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Despite the recent success of Graph Neural Networks (GNNs), training GNNs on large graphs remains challenging. The limited resource capacities of the existing servers, the dependency between nodes in a graph, and the privacy concern due to the centralized storage and model learning have spurred the need to design an effective distributed algorithm for GNN training. However, existing distributed GNN training methods impose either excessive communication costs or large memory overheads that hinders their scalability. To overcome these issues, we propose a communication-efficient distributed GNN training technique named Learn Locally, Correct Globally (LLCG). To reduce the communication and memory overhead, each local machine in LLCG first trains a GNN on its local data by ignoring the dependency between nodes among different machines, then sends the locally trained model to the server for periodic model averaging. However, ignoring node dependency could result in significant performance degradation. To solve the performance degradation, we propose to apply Global Server Corrections on the server to refine the locally learned models. We rigorously analyze the convergence of distributed methods with periodic model averaging for training GNNs and show that naively applying periodic model averaging but ignoring the dependency between nodes will suffer from an irreducible residual error. However, this residual error can be eliminated by utilizing the proposed global corrections to entail fast convergence rate. Extensive experiments on real-world datasets show that LLCG can significantly improve the efficiency without hurting the performance.