scholarly journals Improved Lipophilicity and Aqueous Solubility Prediction with Composite Graph Neural Networks

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6185
Author(s):  
Oliver Wieder ◽  
Mélaine Kuenemann ◽  
Marcus Wieder ◽  
Thomas Seidel ◽  
Christophe Meyer ◽  
...  
Keyword(s):  
Neural Networks ◽  
Performance Metrics ◽  
Graph Isomorphism ◽  
Aqueous Solubility ◽  
Solubility Prediction ◽  
Robust Solution ◽  
Composite Graph ◽  
Edge Graph ◽  
Graph Neural Networks ◽  
Key Aspects

The accurate prediction of molecular properties, such as lipophilicity and aqueous solubility, are of great importance and pose challenges in several stages of the drug discovery pipeline. Machine learning methods, such as graph-based neural networks (GNNs), have shown exceptionally good performance in predicting these properties. In this work, we introduce a novel GNN architecture, called directed edge graph isomorphism network (D-GIN). It is composed of two distinct sub-architectures (D-MPNN, GIN) and achieves an improvement in accuracy over its sub-architectures employing various learning, and featurization strategies. We argue that combining models with different key aspects help make graph neural networks deeper and simultaneously increase their predictive power. Furthermore, we address current limitations in assessment of deep-learning models, namely, comparison of single training run performance metrics, and offer a more robust solution.

scholarly journals Improved Lipophilicity and Aqueous Solubility Prediction With Composite Graph Neural Networks

2021 ◽  
Author(s):  
Oliver Wieder ◽  
Mélaine Kuenemann ◽  
Marcus Wieder ◽  
Thomas Seidel ◽  
Christophe Meyer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Network Architecture ◽  
Performance Metrics ◽  
Aqueous Solubility ◽  
Solubility Prediction ◽  
Machine Learning Model ◽  
Composite Graph ◽  
Graph Neural Networks ◽  
Key Aspects

The accurate prediction of molecular properties such as lipophilicity and aqueous solubility is of great importance in several stages of the drug discovery pipeline. Machine learning methods like graph-based neural networks have shown exceptionally good performance in predicting these properties. In this work we introduce a novel graph neural network architecture composed of two distinct sub-architectures that achieves an improvement in accuracy over its individual parts employing various learning-, and featurization strategies. We argue that combining models with different key aspects might help make graph neural networks deeper while simultaneously increasing their predictive power. Additionally, we want to highlight the need to move beyond comparing single performance metrics to show machine learning model superiority.

scholarly journals Weisfeiler and Leman Go Neural: Higher-Order Graph Neural Networks

2019 ◽  
Vol 33 ◽  
pp. 4602-4609 ◽  
Author(s):  
Christopher Morris ◽  
Martin Ritzert ◽  
Matthias Fey ◽  
William L. Hamilton ◽  
Jan Eric Lenssen ◽  
...  
Keyword(s):  
Neural Networks ◽  
Multiple Scales ◽  
Graph Isomorphism ◽  
Higher Order ◽  
Point Of View ◽  
Theoretical Point ◽  
Graph Classification ◽  
Graph Neural Networks ◽  
Vector Representations

In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically—showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the 1-dimensional Weisfeiler-Leman graph isomorphism heuristic (1-WL). We show that GNNs have the same expressiveness as the 1-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcomings. Based on this, we propose a generalization of GNNs, so-called k-dimensional GNNs (k-GNNs), which can take higher-order graph structures at multiple scales into account. These higher-order structures play an essential role in the characterization of social networks and molecule graphs. Our experimental evaluation confirms our theoretical findings as well as confirms that higher-order information is useful in the task of graph classification and regression.

scholarly journals The Surprising Power of Graph Neural Networks with Random Node Initialization

2021 ◽  
Author(s):  
Ralph Abboud ◽  
İsmail İlkan Ceylan ◽  
Martin Grohe ◽  
Thomas Lukasiewicz
Keyword(s):  
Neural Networks ◽  
Graph Isomorphism ◽  
Expressive Power ◽  
Representation Learning ◽  
Superior Performance ◽  
Initial Node ◽  
Invariance Properties ◽  
Random Node ◽  
Graph Neural Networks ◽  
Effective Models

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

scholarly journals Multi-hop Attention Graph Neural Networks

2021 ◽  
Author(s):  
Guangtao Wang ◽  
Rex Ying ◽  
Jing Huang ◽  
Jure Leskovec
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Performance Metrics ◽  
State Of The Art ◽  
Structural Information ◽  
Representation Learning ◽  
Attention Mechanism ◽  
Graph Representation ◽  
Knowledge Graph ◽  
Graph Neural Networks

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely on the representation of the two nodes. However, such attention mechanism does not account for nodes that are not directly connected but provide important network context. Here we propose Multi-hop Attention Graph Neural Network (MAGNA), a principled way to incorporate multi-hop context information into every layer of attention computation. MAGNA diffuses the attention scores across the network, which increases the receptive field for every layer of the GNN. Unlike previous approaches, MAGNA uses a diffusion prior on attention values, to efficiently account for all paths between the pair of disconnected nodes. We demonstrate in theory and experiments that MAGNA captures large-scale structural information in every layer, and has a low-pass effect that eliminates noisy high-frequency information from graph data. Experimental results on node classification as well as the knowledge graph completion benchmarks show that MAGNA achieves state-of-the-art results: MAGNA achieves up to 5.7% relative error reduction over the previous state-of-the-art on Cora, Citeseer, and Pubmed. MAGNA also obtains the best performance on a large-scale Open Graph Benchmark dataset. On knowledge graph completion MAGNA advances state-of-the-art on WN18RR and FB15k-237 across four different performance metrics.

Graph Neural Networks for Prediction of Fuel Ignition Quality

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>

Conversational Emotion Recognition Using Self-Attention Mechanisms and Graph Neural Networks

2020 ◽  
Author(s):  
Zheng Lian ◽  
Jianhua Tao ◽  
Bin Liu ◽  
Jian Huang ◽  
Zhanlei Yang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Emotion Recognition ◽  
Graph Neural Networks
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