Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex phenomenon of co-evolution between node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and evolution of graph structure over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence of attributed graphs. It has a temporal self-attention architecture to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperforms strong baseline methods on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

The spread of COVID-19 throughout the world has led to cataclysmic consequences on the global community, which poses an urgent need to accurately understand and predict the trajectories of the pandemic. Existing research has relied on graph-structured human mobility data for the task of pandemic forecasting. To perform pandemic forecasting of COVID-19 in the United States, we curate Large-MG, a large-scale mobility dataset that contains 66 dynamic mobility graphs, with each graph having over 3k nodes and an average of 540k edges. One drawback with existing Graph Neural Networks (GNNs) for pandemic forecasting is that they generally perform information propagation in a flat way and thus ignore the inherent community structure in a mobility graph. To bridge this gap, we propose a Hierarchical Spatio-Temporal Graph Neural Network (HiSTGNN) to perform pandemic forecasting, which learns both spatial and temporal information from a sequence of dynamic mobility graphs. HiSTGNN consists of two network architectures. One is a hierarchical graph neural network (HiGNN) that constructs a two-level neural architecture: county-level and region-level, and performs information propagation in a hierarchical way. The other network architecture is a Transformer-based model that captures the temporal dynamics among the sequence of learned node representations from HiGNN. Additionally, we introduce a joint learning objective to further optimize HiSTGNN. Extensive experiments have demonstrated HiSTGNN's superior predictive power of COVID-19 new case/death counts compared with state-of-the-art baselines.

Learning effective recipe representations is essential in food studies. Unlike what has been developed for image-based recipe retrieval or learning structural text embeddings, the combined effect of multi-modal information (i.e., recipe images, text, and relation data) receives less attention. In this paper, we formalize the problem of multi-modal recipe representation learning to integrate the visual, textual, and relational information into recipe embeddings. In particular, we first present Large-RG, a new recipe graph data with over half a million nodes, making it the largest recipe graph to date. We then propose Recipe2Vec, a novel graph neural network based recipe embedding model to capture multi-modal information. Additionally, we introduce an adversarial attack strategy to ensure stable learning and improve performance. Finally, we design a joint objective function of node classification and adversarial learning to optimize the model. Extensive experiments demonstrate that Recipe2Vec outperforms state-of-the-art baselines on two classic food study tasks, i.e., cuisine category classification and region prediction. Dataset and codes are available at https://github.com/meettyj/Recipe2Vec.

CyberPhysical systems (CPS) must be closely monitored to identify and potentially mitigate emergent problems that arise during their routine operations. However, the multivariate time-series data which they typically produce can be complex to understand and analyze. While formal product documentation often provides example data plots with diagnostic suggestions, the sheer diversity of attributes, critical thresholds, and data interactions can be overwhelming to non-experts who subsequently seek help from discussion forums to interpret their data logs. Deep learning models, such as Long Short-term memory (LSTM) networks can be used to automate these tasks and to provide clear explanations of diverse anomalies detected in real-time multivariate data-streams. In this paper we present RESAM, a requirements process that integrates knowledge from domain experts, discussion forums, and formal product documentation, to discover and specify requirements and design definitions in the form of time-series attributes that contribute to the construction of effective deep learning anomaly detectors. We present a case-study based on a flight control system for small Uncrewed Aerial Systems and demonstrate that its use guides the construction of effective anomaly detection models whilst also providing underlying support for explainability. RESAM is relevant to domains in which open or closed online forums provide discussion support for log analysis.