Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to computing ground-state 3D molecular geometries from 2D graphs is lacking. Here, we propose a novel deep learning framework to predict 3D geometries from molecular graphs. To this end, we develop an equilibrium message passing neural network (EMPNN) to better capture ground-state geometries from molecular graphs. To provide a testbed for 3D molecular geometry analysis, we develop a benchmark that includes a dataset with precise ground-state geometries of approximately 4 million molecules. Experimental results show that EMPNN can efficiently predict more accurate ground-state 3D geometries than RDKit and other deep learning methods. Results also show that the proposed framework outperforms self-supervised learning methods on property prediction tasks.

We consider the prediction of the Hamiltonian matrix, which finds use in quantum chemistry and condensed matter physics. Efficiency and equivariance are two important, but conflicting factors. In this work, we propose a SE(3)-equivariant network, named QHNet, that achieves efficiency and equivariance. Our key advance lies at the innovative design of QHNet architecture, which not only obeys the underlying symmetries, but also enables the reduction of number of tensor products by 92%. In addition, QHNet prevents the exponential growth of channel dimension when more atom types are involved. We perform experiments on MD17 datasets, including four molecular systems. Experimental results show that our QHNet can achieve comparable performance to the state of the art methods at a significantly faster speed. Besides, our QHNet consumes 50% less memory due to its streamlined architecture. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.

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.

This tutorial is proposed based upon the recently released open-source library Dive into Graphs (DIG) along with hands-on code examples. DIG is a turnkey library that considers four frontiers in graph deep learning, including self-supervised learning of GNNs, 3D GNNs, explainability of GNNs, and graph generation. It provides data interfaces, common algorithms, and evaluation metrics for each direction. It has 255,000+ visitors, 11,000+ installations, and 1,100+ stars within a year and is becoming a robust and dominant ecosystem for graph neural network research. In this tutorial, we will review representative methodologies for these four directions and show hands-on code examples to demonstrate how to effortlessly implement benchmarks using DIG. This tutorial targets a broad audience working on or interested in various research themes. To encourage audience participation, we will promote our tutorial in advance on social media, reading groups, and library contribution community. We anticipate this tutorial would attract more researchers to these interesting and promising topics, leading to a more active community, eventually generating both scientific values and real-world impacts.

MOTIVATION: Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep-learning methods, computational approaches for predicting molecular properties are gaining increasing momentum. However, there lacks customized and advanced methods and comprehensive tools for this task currently. RESULTS: Here, we develop a suite of comprehensive machine-learning methods and tools spanning different computational models, molecular representations and loss functions for molecular property prediction and drug discovery. Specifically, we represent molecules as both graphs and sequences. Built on these representations, we develop novel deep models for learning from molecular graphs and sequences. In order to learn effectively from highly imbalanced datasets, we develop advanced loss functions that optimize areas under precision-recall curves (PRCs) and receiver operating characteristic (ROC) curves. Altogether, our work not only serves as a comprehensive tool, but also contributes toward developing novel and advanced graph and sequence-learning methodologies. Results on both online and offline antibiotics discovery and molecular property prediction tasks show that our methods achieve consistent improvements over prior methods. In particular, our methods achieve #1 ranking in terms of both ROC-AUC (area under curve) and PRC-AUC on the AI Cures open challenge for drug discovery related to COVID-19. AVAILABILITY AND IMPLEMENTATION: Our source code is released as part of the MoleculeX library (https://github.com/divelab/MoleculeX) under AdvProp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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 stochastic optimization of AUROC has been studied extensively, principled stochastic 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 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 named SOAP with provable convergence guarantee under mild conditions by leveraging recent advances in stochastic compositional optimization. Extensive experimental results on image and graph datasets demonstrate that our proposed method outperforms prior methods on imbalanced problems in terms of AUPRC. To the best of our knowledge, our work represents the first attempt to optimize AUPRC with provable convergence. The SOAP has been implemented in the libAUC library at https://libauc.org/.

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.