Automated Data Augmentations for Graph Classification

Data augmentations are effective in improving the invariance of learning machines. We argue that the corechallenge of data augmentations lies in designing data transformations that preserve labels. This is relativelystraightforward for images, but much more challenging for graphs. In this work, we propose GraphAug, a novelautomated data augmentation method aiming at computing label-invariant augmentations for graph classification.Instead of using uniform transformations as in existing studies, GraphAug uses an automated augmentationmodel to avoid compromising critical label-related information of the graph, thereby producing label-invariantaugmentations at most times. To ensure label-invariance, we develop a training method based on reinforcementlearning to maximize an estimated label-invariance probability. Comprehensive experiments show that GraphAugoutperforms previous graph augmentation methods on various graph classification tasks.

Task-Agnostic Graph Explanations

Graph Neural Networks (GNNs) have emerged as powerful tools to encode graph structured data. Due to their broad applications, there is an increasing need to develop tools to explain how GNNs make decisions given graph structured data. Existing learning-based GNN explanation approaches are task-specific in training and hence suffer from crucial drawbacks. Specifically, they are incapable of producing explanations for a multitask prediction model with a single explainer. They are also unable to provide explanations in cases where the GNN is trained in a self-supervised manner, and the resulting representations are used in future downstream tasks. To address these limitations, we propose a Task-Agnostic GNN Explainer (TAGE) trained under self-supervision with no knowledge of downstream tasks. TAGE enables the explanation of GNN embedding models without downstream tasks and allows efficient explanation of multitask models. Our extensive experiments show that TAGE can significantly speed up the explanation efficiency by using the same model to explain predictions for multiple downstream tasks while achieving explanation quality as good as or even better than current state-of-the-art GNN explanation approaches.

Self-Supervised Representation Learning via Latent Graph Prediction

Self-supervised learning (SSL) of graph neural networks is emerging as a promising way of leveraging unlabeled data. Currently, most methods are based on contrastive learning adapted from the image domain, which requires view generation and a sufficient number of negative samples. In contrast, existing predictive models do not require negative sampling, but lack theoretical guidance on the design of pretext training tasks. In this work, we propose the LaGraph, a theoretically grounded predictive SSL framework based on latent graph prediction. Learning objectives of LaGraph are derived as self-supervised upper bounds to objectives for predicting unobserved latent graphs. In addition to its improved performance, LaGraph provides explanations for recent successes of predictive models that include invariance-based objectives. We provide theoretical analysis comparing LaGraph to related methods in different domains. Our experimental results demonstrate the superiority of LaGraph in performance and the robustness to decreasing of training sample size on both graph-level and node-level tasks.

Neighbor2Seq: Deep Learning on Massive Graphs by Transforming Neighbors to Sequences

Modern graph neural networks (GNNs) use a message passing scheme and have achieved great success in many fields. However, this recursive design inherently leads to excessive computation and memory requirements, making it not applicable to massive real-world graphs. In this work, we propose the Neighbor2Seq to transform the hierarchical neighborhood of each node into a sequence. This novel transformation enables the subsequent mini-batch training for general deep learning operations, such as convolution and attention, that are designed for grid-like data and are shown to be powerful in various domains. Therefore, our Neighbor2Seq naturally endows GNNs with the efficiency and advantages of deep learning operations on grid-like data by precomputing the Neighbor2Seq transformations. We evaluate our method on a massive graph, with more than 111 million nodes and 1.6 billion edges, as well as several medium-scale graphs. Results show that our proposed method is scalable to massive graphs and achieves superior performance across massive and medium-scale graphs. Our code is available at https://github.com/divelab/Neighbor2Seq.

ConE: Cone Embeddings for Multi-Hop Reasoning over Knowledge Graphs

Query embedding (QE) -- which aims to embed entities and first-order logical (FOL) queries in low-dimensional spaces -- has shown great power in multi-hop reasoning over knowledge graphs. Recently, embedding entities and queries with geometric shapes becomes a promising direction, as geometric shapes can naturally represent answer sets of queries and logical relationships among them. However, existing geometry-based models have difficulty in modeling queries with negation, which significantly limits their applicability. To address this challenge, we propose a novel query embedding model, namely Cone Embeddings (ConE), which is the first geometry-based QE model that can handle all the FOL operations, including conjunction, disjunction, and negation. Specifically, ConE represents entities and queries as Cartesian products of two-dimensional cones, where the intersection and union of cones naturally model the conjunction and disjunction operations. By further noticing that the closure of complement of cones remains cones, we design geometric complement operators in the embedding space for the negation operations. Experiments demonstrate that ConE significantly outperforms existing state-of-the-art methods on benchmark datasets.

Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Group Contrastive Self-Supervised Learning on Graphs

We study self-supervised learning on graphs using contrastive methods. A general scheme of prior methods is to optimize two-view representations of input graphs. In many studies, a single graph-level representation is computed as one of the contrastive objectives, capturing limited characteristics of graphs. We argue that contrasting graphs in multiple subspaces enables graph encoders to capture more abundant characteristics. To this end, we propose a group contrastive learning framework in this work. Our framework embeds the given graph into multiple subspaces, of which each representation is prompted to encode specific characteristics of graphs. To learn diverse and informative representations, we develop principled objectives that enable us to capture the relations among both intra-space and inter-space representations in groups. Under the proposed framework, we further develop an attention-based representor function to compute representations that capture different substructures of a given graph. Built upon our framework, we extend two current methods into GroupCL and GroupIG, equipped with the proposed objective. Comprehensive experimental results show our framework achieves a promising boost in performance on a variety of datasets. In addition, our qualitative results show that features generated from our representor successfully capture various specific characteristics of graphs.

Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks

Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically favorable since obtaining 3D equilibrium structures requires extremely expensive calculations. In this work, we design a deep graph neural network to predict quantum properties by directly learning from 2D molecular graphs. In addition, we propose a 3D graph neural network to learn from low-cost conformer sets, which can be obtained with open-source tools using an affordable budget. We employ our methods to participate in the 2021 KDD Cup on OGB Large-Scale Challenge (OGB-LSC), which aims to predict the HOMO-LUMO energy gap of molecules. Final evaluation results reveal that we are one of the winners with a mean absolute error of 0.1235 on the holdout test set. Our implementation is available as part of the MoleculeX package (https://github.com/divelab/MoleculeX).

Graph Neural Networks with Adaptive Frequency Response Filter

Graph Neural Networks have recently become a prevailing paradigm for various high-impact graph learning tasks. Existing efforts can be mainly categorized as spectral-based and spatial-based methods. The major challenge for the former is to find an appropriate graph filter to distill discriminative information from input signals for learning. Recently, attempts such as Graph Convolutional Network (GCN) leverage Chebyshev polynomial truncation to seek an approximation of graph filters and bridge these two families of methods. It has been shown in recent studies that GCN and its variants are essentially employing fixed low-pass filters to perform information denoising. Thus their learning capability is rather limited and may over-smooth node representations at deeper layers. To tackle these problems, we develop a novel graph neural network framework AdaGNN with a well-designed adaptive frequency response filter. At its core, AdaGNN leverages a simple but elegant trainable filter that spans across multiple layers to capture the varying importance of different frequency components for node representation learning. The inherent differences among different feature channels are also well captured by the filter. As such, it empowers AdaGNN with stronger expressiveness and naturally alleviates the over-smoothing problem. We empirically validate the effectiveness of the proposed framework on various benchmark datasets. Theoretical analysis is also provided to show the superiority of the proposed AdaGNN. The implementation of AdaGNN is available at \url{https://github.com/yushundong/AdaGNN}.

Stochastic Optimization of Area Under Precision-Recall Curve for Deep Learning with Provable Convergence

Areas under ROC (AUROC) and precision-recall curves (AUPRC) are common metrics for evaluating classification performance for imbalanced problems. Compared with AUROC, AUPRC is a more appropriate metric for highly imbalanced datasets. While direct optimization of AUROC has been studied extensively, optimization of AUPRC has been rarely explored. In this work, we propose a principled technical method to optimize AUPRC for deep learning. Our approach is based on maximizing the averaged precision (AP), which is an unbiased point estimator of AUPRC. We show that the surrogate loss function for AP is highly non-convex and more complicated than that of AUROC. We cast the objective into a sum of dependent compositional functions with inner functions dependent on random variables of the outer level. We propose efficient adaptive and non-adaptive stochastic algorithms with provable convergence guarantee under mild conditions by using recent advances in stochastic compositional optimization. Extensive experimental results on graphs and image datasets demonstrate that our proposed method outperforms prior methods on imbalanced problems. To the best of our knowledge, our work represents the first attempt to optimize AUPRC with provable convergence.