Predicting vulnerability inducing function versions using node embeddings and graph neural networks

Graph Neural Networks (GNNs) rely on the graph structure to define an aggregation strategy where each node updates its representation by combining information from its neighbours. A known limitation of GNNs is that, as the number of layers increases, information gets smoothed and squashed and node embeddings become indistinguishable, negatively affecting performance. Therefore, practical GNN models employ few layers and only leverage the graph structure in terms of limited, small neighbourhoods around each node. Inevitably, practical GNNs do not capture information depending on the global structure of the graph. While there have been several works studying the limitations and expressivity of GNNs, the question of whether practical applications on graph structured data require global structural knowledge or not remains unanswered. In this work, we empirically address this question by giving access to global information to several GNN models, and observing the impact it has on downstream performance. Our results show that global information can in fact provide significant benefits for common graph-related tasks. We further identify a novel regularization strategy that leads to an average accuracy improvement of more than 5% on all considered tasks.

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GraphReach: Position-Aware Graph Neural Network using Reachability Estimations

Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence ◽

10.24963/ijcai.2021/211 ◽

2021 ◽

Author(s):

Sunil Nishad ◽

Shubhangi Agarwal ◽

Arnab Bhattacharya ◽

Sayan Ranu

Keyword(s):

Neural Network ◽

Neural Networks ◽

State Of The Art ◽

Empirical Evaluation ◽

Position Information ◽

Accurate Performance ◽

Anchor Nodes ◽

Approximation Heuristic ◽

Graph Neural Networks ◽

Node Embeddings

Majority of the existing graph neural networks(GNN) learn node embeddings that encode their local neighborhoods but not their positions. Consequently, two nodes that are vastly distant but located in similar local neighborhoods map to similar embeddings in those networks. This limitation prevents accurate performance in predictive tasks that rely on position information. In this paper, we develop GRAPHREACH , a position-aware inductive GNN that captures the global positions of nodes through reachability estimations with respect to a set of anchor nodes. The anchors are strategically selected so that reachability estimations across all the nodes are maximized. We show that this combinatorial anchor selection problem is NP-hard and, consequently, develop a greedy (1−1/e) approximation heuristic. Empirical evaluation against state-of-the-art GNN architectures reveal that GRAPHREACH provides up to 40% relative improvement in accuracy. In addition, it is more robust to adversarial attacks.

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Graph Neural Networks for Prediction of Fuel Ignition Quality

10.26434/chemrxiv.12280325.v1 ◽

2020 ◽

Author(s):

Artur Schweidtmann ◽

Jan Rittig ◽

Andrea König ◽

Martin Grohe ◽

Alexander Mitsos ◽

...

Keyword(s):

Neural Networks ◽

Octane Number ◽

Molecular Graph ◽

Chemical Properties ◽

Graph Representation ◽

Structure Property ◽

Oxygenated Hydrocarbons ◽

Physico Chemical ◽

Ignition Quality ◽

Graph Neural Networks

<div>Prediction of combustion-related properties of (oxygenated) hydrocarbons is an important and challenging task for which quantitative structure-property relationship (QSPR) models are frequently employed. Recently, a machine learning method, graph neural networks (GNNs), has shown promising results for the prediction of structure-property relationships. GNNs utilize a graph representation of molecules, where atoms correspond to nodes and bonds to edges containing information about the molecular structure. More specifically, GNNs learn physico-chemical properties as a function of the molecular graph in a supervised learning setup using a backpropagation algorithm. This end-to-end learning approach eliminates the need for selection of molecular descriptors or structural groups, as it learns optimal fingerprints through graph convolutions and maps the fingerprints to the physico-chemical properties by deep learning. We develop GNN models for predicting three fuel ignition quality indicators, i.e., the derived cetane number (DCN), the research octane number (RON), and the motor octane number (MON), of oxygenated and non-oxygenated hydrocarbons. In light of limited experimental data in the order of hundreds, we propose a combination of multi-task learning, transfer learning, and ensemble learning. The results show competitive performance of the proposed GNN approach compared to state-of-the-art QSPR models making it a promising field for future research. The prediction tool is available via a web front-end at www.avt.rwth-aachen.de/gnn.</div>

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