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Over the past decade, Graph Neural Networks (GNNs) have transformed graph representation learning. In the widely adopted message-passing GNN framework, nodes refine their representations by aggregating information from neighboring nodes iteratively. While GNNs excel in various domains, recent theoretical studies have raised concerns about their capabilities. GNNs aim to address various graph-related tasks by utilizing such node representations, however, this one-size-fits-all approach proves suboptimal for diverse tasks. Motivated by these observations, we conduct empirical tests to compare the performance of current GNN models with more conventional and direct methods in link prediction tasks. Introducing our model, PROXI, which leverages proximity information of node pairs in both graph and attribute spaces, we find that standard machine learning (ML) models perform competitively, even outperforming cutting-edge GNN models when applied to these proximity metrics derived from node neighborhoods and attributes. This holds true across both homophilic and heterophilic networks, as well as small and large benchmark datasets, including those from the Open Graph Benchmark (OGB). Moreover, we show that augmenting traditional GNNs with PROXI significantly boosts their link prediction performance. Our empirical findings corroborate the previously mentioned theoretical observations and imply that there exists ample room for enhancement in current GNN models to reach their potential. 

This dataset compiles the results of our study of nuclear quantum effects (NQEs) and equilibrium isotope effects (EIEs) of 92 chemically diverse, organic molecular liquids. It contains the average macroscopic properties (density, molar volume, thermal expansion coefficient, isothermal compressibility, dielectric constant, heat of vaporization) and their associated standard errors computed with four independent classical and path-integral molecular dynamics (PIMD) simulations of each system and their deuterated counterparts. All simulations use the Topology Automated Force-Field Interactions (TAFFI) framework to describe the potential energy surface. In addition, the computed nuclear quantum effects and equilibrium isotope effects resulting from comparison of these simulations are included. 

Many real-world networks evolve over time, and predicting the evolution of such networks remains a challenging task. Graph Neural Networks (GNNs) have shown empirical success for learning on static graphs, but they lack the ability to effectively learn from nodes and edges with different timestamps. Consequently, the prediction of future properties in temporal graphs remains a relatively under-explored area. In this paper, we aim to bridge this gap by introducing a principled framework, named GraphPulse. The framework combines two important techniques for the analysis of temporal graphs within a Newtonian framework. First, we employ the Mapper method, a key tool in topological data analysis, to extract essential clustering information from graph nodes. Next, we harness the sequential modeling capabilities of Recurrent Neural Networks (RNNs) for temporal reasoning regarding the graph's evolution. Through extensive experimentation, we demonstrate that our model enhances the ROC-AUC metric by 10.2% in comparison to the top-performing state-of-the-art method across various temporal networks. We provide the implementation of GraphPulse at https://github.com/kiarashamsi/GraphPulse.