scholarly journals Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks

Author(s):  
Joseph D. Romano ◽  
Yun Hao ◽  
Jason H. Moore
2021 ◽  
Author(s):  
Joseph D Romano ◽  
Yun Hao ◽  
Jason H Moore

Quantitative Structure-Activity Relationship (QSAR) modeling is the most common computational technique for predicting chemical toxicity, but a lack of methodological innovations in QSAR have led to underwhelming performance. We show that contemporary QSAR modeling for predictive toxicology can be substantially improved by incorporating semantic graph data aggregated from open-access public databases, and analyzing those data in the context of graph neural networks (GNNs). Furthermore, we introspect the GNNs to demonstrate how they can lead to more interpretable applications of QSAR, and use ablation analysis to explore the contribution of different data elements to the final models' performance.


Author(s):  
Jiafeng Cheng ◽  
Qianqian Wang ◽  
Zhiqiang Tao ◽  
Deyan Xie ◽  
Quanxue Gao

Graph neural networks (GNNs) have made considerable achievements in processing graph-structured data. However, existing methods can not allocate learnable weights to different nodes in the neighborhood and lack of robustness on account of neglecting both node attributes and graph reconstruction. Moreover, most of multi-view GNNs mainly focus on the case of multiple graphs, while designing GNNs for solving graph-structured data of multi-view attributes is still under-explored. In this paper, we propose a novel Multi-View Attribute Graph Convolution Networks (MAGCN) model for the clustering task. MAGCN is designed with two-pathway encoders that map graph embedding features and learn the view-consistency information. Specifically, the first pathway develops multi-view attribute graph attention networks to reduce the noise/redundancy and learn the graph embedding features for each multi-view graph data. The second pathway develops consistent embedding encoders to capture the geometric relationship and probability distribution consistency among different views, which adaptively finds a consistent clustering embedding space for multi-view attributes. Experiments on three benchmark graph datasets show the superiority of our method compared with several state-of-the-art algorithms.


Author(s):  
Kaidi Xu ◽  
Hongge Chen ◽  
Sijia Liu ◽  
Pin-Yu Chen ◽  
Tsui-Wei Weng ◽  
...  

Graph neural networks (GNNs) which apply the deep neural networks to graph data have achieved significant performance for the task of semi-supervised node classification. However, only few work has addressed the adversarial robustness of GNNs. In this paper, we first present a novel gradient-based attack method that facilitates the difficulty of tackling discrete graph data. When comparing to current adversarial attacks on GNNs, the results show that by only perturbing a small number of edge perturbations, including addition and deletion, our optimization-based attack can lead to a noticeable decrease in classification performance. Moreover, leveraging our gradient-based attack, we propose the first optimization-based adversarial training for GNNs. Our method yields higher robustness against both different gradient based and greedy attack methods without sacrifice classification accuracy on original graph.


Author(s):  
Xiang Deng ◽  
Zhongfei Zhang

Knowledge distillation (KD) transfers knowledge from a teacher network to a student by enforcing the student to mimic the outputs of the pretrained teacher on training data. However, data samples are not always accessible in many cases due to large data sizes, privacy, or confidentiality. Many efforts have been made on addressing this problem for convolutional neural networks (CNNs) whose inputs lie in a grid domain within a continuous space such as images and videos, but largely overlook graph neural networks (GNNs) that handle non-grid data with different topology structures within a discrete space. The inherent differences between their inputs make these CNN-based approaches not applicable to GNNs. In this paper, we propose to our best knowledge the first dedicated approach to distilling knowledge from a GNN without graph data. The proposed graph-free KD (GFKD) learns graph topology structures for knowledge transfer by modeling them with multinomial distribution. We then introduce a gradient estimator to optimize this framework. Essentially, the gradients w.r.t. graph structures are obtained by only using GNN forward-propagation without back-propagation, which means that GFKD is compatible with modern GNN libraries such as DGL and Geometric. Moreover, we provide the strategies for handling different types of prior knowledge in the graph data or the GNNs. Extensive experiments demonstrate that GFKD achieves the state-of-the-art performance for distilling knowledge from GNNs without training data.


2021 ◽  
Vol 55 (1) ◽  
pp. 68-76
Author(s):  
Marco Serafini

Graph Neural Networks (GNNs) are a new and increasingly popular family of deep neural network architectures to perform learning on graphs. Training them efficiently is challenging due to the irregular nature of graph data. The problem becomes even more challenging when scaling to large graphs that exceed the capacity of single devices. Standard approaches to distributed DNN training, like data and model parallelism, do not directly apply to GNNs. Instead, two different approaches have emerged in the literature: whole-graph and sample-based training. In this paper, we review and compare the two approaches. Scalability is challenging with both approaches, but we make a case that research should focus on sample-based training since it is a more promising approach. Finally, we review recent systems supporting sample-based training.


2022 ◽  
Vol 40 (4) ◽  
pp. 1-46
Author(s):  
Hao Peng ◽  
Ruitong Zhang ◽  
Yingtong Dou ◽  
Renyu Yang ◽  
Jingyi Zhang ◽  
...  

Graph Neural Networks (GNNs) have been widely used for the representation learning of various structured graph data, typically through message passing among nodes by aggregating their neighborhood information via different operations. While promising, most existing GNNs oversimplify the complexity and diversity of the edges in the graph and thus are inefficient to cope with ubiquitous heterogeneous graphs, which are typically in the form of multi-relational graph representations. In this article, we propose RioGNN , a novel Reinforced, recursive, and flexible neighborhood selection guided multi-relational Graph Neural Network architecture, to navigate complexity of neural network structures whilst maintaining relation-dependent representations. We first construct a multi-relational graph, according to the practical task, to reflect the heterogeneity of nodes, edges, attributes, and labels. To avoid the embedding over-assimilation among different types of nodes, we employ a label-aware neural similarity measure to ascertain the most similar neighbors based on node attributes. A reinforced relation-aware neighbor selection mechanism is developed to choose the most similar neighbors of a targeting node within a relation before aggregating all neighborhood information from different relations to obtain the eventual node embedding. Particularly, to improve the efficiency of neighbor selecting, we propose a new recursive and scalable reinforcement learning framework with estimable depth and width for different scales of multi-relational graphs. RioGNN can learn more discriminative node embedding with enhanced explainability due to the recognition of individual importance of each relation via the filtering threshold mechanism. Comprehensive experiments on real-world graph data and practical tasks demonstrate the advancements of effectiveness, efficiency, and the model explainability, as opposed to other comparative GNN models.


2021 ◽  
Vol 11 (19) ◽  
pp. 9055
Author(s):  
Ce Guo ◽  
Pengming Zhu ◽  
Zhiqian Zhou ◽  
Lin Lang ◽  
Zhiwen Zeng ◽  
...  

This paper focuses on generating distributed flocking strategies via imitation learning. The primary motivation is to improve the swarm robustness and achieve better consistency while respecting the communication constraints. This paper first proposes a quantitative metric of swarm robustness based on entropy evaluation. Then, the graph importance consistency is also proposed, which is one of the critical goals of the flocking task. Moreover, the importance-correlated directed graph convolutional networks (IDGCNs) are constructed for multidimensional feature extraction and structure-related aggregation of graph data. Next, by employing IDGCNs-based imitation learning, a distributed and scalable flocking strategy is obtained, and its performance is very close to the centralized strategy template while considering communication constraints. To speed up and simplify the training process, we train the flocking strategy with a small number of agents and set restrictions on communication. Finally, various simulation experiments are executed to verify the advantages of the obtained strategy in terms of realizing the swarm consistency and improving the swarm robustness. The results also show that the performance is well maintained while the scale of agents expands (tested with 20, 30, 40 robots).


Author(s):  
Ziqi Liu ◽  
Chaochao Chen ◽  
Longfei Li ◽  
Jun Zhou ◽  
Xiaolong Li ◽  
...  

We present, GeniePath, a scalable approach for learning adaptive receptive fields of neural networks defined on permutation invariant graph data. In GeniePath, we propose an adaptive path layer consists of two complementary functions designed for breadth and depth exploration respectively, where the former learns the importance of different sized neighborhoods, while the latter extracts and filters signals aggregated from neighbors of different hops away. Our method works in both transductive and inductive settings, and extensive experiments compared with competitive methods show that our approaches yield state-of-the-art results on large graphs.


2020 ◽  
Author(s):  
Artur Schweidtmann ◽  
Jan Rittig ◽  
Andrea König ◽  
Martin Grohe ◽  
Alexander Mitsos ◽  
...  

<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>


2020 ◽  
Author(s):  
Zheng Lian ◽  
Jianhua Tao ◽  
Bin Liu ◽  
Jian Huang ◽  
Zhanlei Yang ◽  
...  

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