Subgraph Neural Networks

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks

Deep learning methods for graphs achieve remarkable performance on many tasks. However, despite the proliferation of such methods and their success, recent findings indicate that small, unnoticeable perturbations of graph structure can catastrophically reduce performance of even the strongest and most popular Graph Neural Networks (GNNs). Here, we develop GNNGuard, a general defense approach against a variety of training-time attacks that perturb the discrete graph structure. GNNGuard can be straightforwardly incorporated into any GNN. Its core principle is to detect and quantify the relationship between the graph structure and node features, if one exists, and then exploit that relationship to mitigate negative effects of the attack. GNNGuard uses network theory of homophily to learn how best assign higher weights to edges connecting similar nodes while pruning edges between unrelated nodes. The revised edges then allow the underlying GNN to robustly propagate neural messages in the graph. GNNGuard introduces two novel components, the neighbor importance estimation, and the layer-wise graph memory, and we show empirically that both components are necessary for a successful defense. Across five GNNs, three defense methods, and four datasets, including a challenging human disease graph, experiments show that GNNGuard outperforms existing defense approaches by 15.3% on average. Remarkably, GNNGuard can effectively restore the state-of-the-art performance of GNNs in the face of various adversarial attacks, including targeted and non-targeted attacks.

Graph Meta Learning via Local Subgraphs

Prevailing methods for graphs require abundant label and edge information for learning. When data for a new task are scarce, meta-learning allows us to learn from prior experiences and form much-needed inductive biases for fast adaption to the new task. Here, we introduce G-Meta, a novel meta-learning approach for graphs. G-Meta uses local subgraphs to transfer subgraph-specific information and make the model learn the essential knowledge faster via meta gradients. G-Meta learns how to quickly adapt to a new task using only a handful of nodes or edges in the new task and does so by learning from data points in other graphs or related, albeit disjoint label sets. G-Meta is theoretically justified as we show that the evidence for a particular prediction can be found in the local subgraph surrounding the target node or edge. G-Meta is theoretically justified, which we show using the theory of enclosing subgraphs. Experiments on seven datasets and nine baseline methods show that G-Meta can considerably outperform existing methods by up to 16.3%. Unlike previous methods, G-Meta can successfully learn in challenging, few-shot learning settings that require generalization to completely new graphs and never-before-seen labels. Finally, G-Meta scales to large graphs, which we demonstrate on our new Tree-of-Life dataset comprising of 1,840 graphs, a two-orders of magnitude increase in the number of graphs used in prior work.

Open Graph Benchmark: Datasets for Machine Learning on Graphs

We present the Open Graph Benchmark (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using application-specific data splits and evaluation metrics. Our empirical investigation reveals the challenges of existing graph methods in handling large-scale graphs and predicting out-of-distribution data. OGB presents an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community. OGB datasets as well as data loaders and evaluation scripts are available at https://ogb.stanford.edu .

SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks

Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the prediction prowess, current graph neural network (GNN) methods are optimized for prediction on the basis of direct similarity between interacting nodes. In biological networks, however, similarity between nodes that do not directly interact has proved incredibly useful in the last decade across a variety of interaction networks. Here, we present SkipGNN, a graph neural network approach for the prediction of molecular interactions. SkipGNN predicts molecular interactions by not only aggregating information from direct interactions but also from second-order interactions, which we call skip similarity. In contrast to existing GNNs, SkipGNN receives neural messages from two-hop neighbors as well as immediate neighbors in the interaction network and non-linearly transforms the messages to obtain useful information for prediction. To inject skip similarity into a GNN, we construct a modified version of the original network, called the skip graph. We then develop an iterative fusion scheme that optimizes a GNN using both the skip graph and the original graph. Experiments on four interaction networks, including drug-drug, drug-target, protein-protein, and gene-disease interactions, show that SkipGNN achieves superior and robust performance, outperforming existing methods by up to 28.8\% of area under the precision recall curve (PR-AUC). Furthermore, we show that unlike popular GNNs, SkipGNN learns biologically meaningful embeddings and performs especially well on noisy, incomplete interaction networks.

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

The COVID-19 pandemic demands the rapid identification of drug-repurpusing candidates. In the past decade, network medicine had developed a framework consisting of a series of quantitative approaches and predictive tools to study host-pathogen interactions, unveil the molecular mechanisms of the infection, identify comorbidities as well as rapidly detect drug repurpusing candidates. Here, we adapt the network-based toolset to COVID-19, recovering the primary pulmonary manifestations of the virus in the lung as well as observed comorbidities associated with cardiovascular diseases. We predict that the virus can manifest itself in other tissues, such as the reproductive system, and brain regions, moreover we predict neurological comorbidities. We build on these findings to deploy three network-based drug repurposing strategies, relying on network proximity, diffusion, and AI-based metrics, allowing to rank all approved drugs based on their likely efficacy for COVID-19 patients, aggregate all predictions, and, thereby to arrive at 81 promising repurposing candidates. We validate the accuracy of our predictions using drugs currently in clinical trials, and an expression-based validation of selected candidates suggests that these drugs, with known toxicities and side effects, could be moved to clinical trials rapidly.

Interpretability of machine learning based prediction models in healthcare

There is a need of ensuring machine learning models that are interpretable. Higher interpretability of the model means easier comprehension and explanation of future predictions for end-users. Further, interpretable machine learning models allow healthcare experts to make reasonable and data-driven decisions to provide personalized decisions that can ultimately lead to higher quality of service in healthcare. Generally, we can classify interpretability approaches in two groups where the first focuses on personalized interpretation (local interpretability) while the second summarizes prediction models on a population level (global interpretability). Alternatively, we can group interpretability methods into model-specific techniques, which are designed to interpret predictions generated by a specific model, such as a neural network, and model-agnostic approaches, which provide easy-to-understand explanations of predictions made by any machine learning model. Here, we give an overview of interpretability approaches and provide examples of practical interpretability of machine learning in different areas of healthcare, including prediction of health-related outcomes, optimizing treatments or improving the efficiency of screening for specific conditions. Further, we outline future directions for interpretable machine learning and highlight the importance of developing algorithmic solutions that can enable machine-learning driven decision making in high-stakes healthcare problems.

Pre-training Graph Neural Networks

Many applications of machine learning in science and medicine, including molecular property and protein function prediction, can be cast as problems of predicting some properties of graphs, where having good graph representations is critical. However, two key challenges in these domains are (1) extreme scarcity of labeled data due to expensive lab experiments, and (2) needing to extrapolate to test graphs that are structurally different from those seen during training. In this paper, we explore pre-training to address both of these challenges. In particular, working with Graph Neural Networks (GNNs) for representation learning of graphs, we wish to obtain node representations that (1) capture similarity of nodes' network neighborhood structure, (2) can be composed to give accurate graph-level representations, and (3) capture domain-knowledge. To achieve these goals, we propose a series of methods to pre-train GNNs at both the node-level and the graph-level, using both unlabeled data and labeled data from related auxiliary supervised tasks. We perform extensive evaluation on two applications, molecular property and protein function prediction. We observe that performing only graph-level supervised pre-training often leads to marginal performance gain or even can worsen the performance compared to non-pre-trained models. On the other hand, effectively combining both node- and graph-level pre-training techniques significantly improves generalization to out-of-distribution graphs, consistently outperforming non-pre-trained GNNs across 8 datasets in molecular property prediction (resp. 40 tasks in protein function prediction), with the average ROC-AUC improvement of 7.2% (resp. 11.7%).

GNN Explainer: A Tool for Post-hoc Explanation of Graph Neural Networks

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by using neural networks to pass messages through edges in the graph. However, incorporating both graph structure and feature information leads to complex non-linear models and explaining predictions made by GNNs remains to be a challenging task. Here we propose GnnExplainer, a general model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task (node and graph classification, link prediction). In order to explain a given node's predicted label, GnnExplainer provides a local interpretation by highlighting relevant features as well as an important subgraph structure by identifying the edges that are most relevant to the prediction. Additionally, the model provides single-instance explanations when given a single prediction as well as multi-instance explanations that aim to explain predictions for an entire class of instances/nodes. We formalize GnnExplainer as an optimization task that maximizes the mutual information between the prediction of the full model and the prediction of simplified explainer model. We experiment on synthetic as well as real-world data. On synthetic data we demonstrate that our approach is able to highlight relevant topological structures from noisy graphs. We also demonstrate GnnExplainer to provide a better understanding of pre-trained models on real-world tasks. GnnExplainer provides a variety of benefits, from the identification of semantically relevant structures to explain predictions to providing guidance when debugging faulty graph neural network models.