Session-based Recommendation with Graph Neural Networks

The problem of session-based recommendation aims to predict user actions based on anonymous sessions. Previous methods model a session as a sequence and estimate user representations besides item representations to make recommendations. Though achieved promising results, they are insufficient to obtain accurate user vectors in sessions and neglect complex transitions of items. To obtain accurate item embedding and take complex transitions of items into account, we propose a novel method, i.e. Session-based Recommendation with Graph Neural Networks, SR-GNN for brevity. In the proposed method, session sequences are modeled as graph-structured data. Based on the session graph, GNN can capture complex transitions of items, which are difficult to be revealed by previous conventional sequential methods. Each session is then represented as the composition of the global preference and the current interest of that session using an attention network. Extensive experiments conducted on two real datasets show that SR-GNN evidently outperforms the state-of-the-art session-based recommendation methods consistently.Comment: 9 pages, 4 figures, accepted by AAAI Conference on Artificial Intelligence (AAAI-19

A Systematic Survey of Chemical Pre-trained Models

Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design. However, training Deep Neural Networks (DNNs) from scratch often requires abundant labeled molecules, which are expensive to acquire in the real world. To alleviate this issue, tremendous efforts have been devoted to Molecular Pre-trained Models (CPMs), where DNNs are pre-trained using large-scale unlabeled molecular databases and then fine-tuned over specific downstream tasks. Despite the prosperity, there lacks a systematic review of this fast-growing field. In this paper, we present the first survey that summarizes the current progress of CPMs. We first highlight the limitations of training molecular representation models from scratch to motivate CPM studies. Next, we systematically review recent advances on this topic from several key perspectives, including molecular descriptors, encoder architectures, pre-training strategies, and applications. We also highlight the challenges and promising avenues for future research, providing a useful resource for both machine learning and scientific communities.Comment: IJCAI 2023, Survey Trac

Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis

Multimodal brain networks characterize complex connectivities among different brain regions from both structural and functional aspects and provide a new means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have become a de facto model for analyzing graph-structured data. However, how to employ GNNs to extract effective representations from brain networks in multiple modalities remains rarely explored. Moreover, as brain networks provide no initial node features, how to design informative node attributes and leverage edge weights for GNNs to learn is left unsolved. To this end, we develop a novel multiview GNN for multimodal brain networks. In particular, we regard each modality as a view for brain networks and employ contrastive learning for multimodal fusion. Then, we propose a GNN model which takes advantage of the message passing scheme by propagating messages based on degree statistics and brain region connectivities. Extensive experiments on two real-world disease datasets (HIV and Bipolar) demonstrate the effectiveness of our proposed method over state-of-the-art baselines.Comment: Accepted to ICML 2021 Workshop on Computational Approaches to Mental Healt

TAGNN: Target Attentive Graph Neural Networks for Session-based Recommendation

Session-based recommendation nowadays plays a vital role in many websites, which aims to predict users' actions based on anonymous sessions. There have emerged many studies that model a session as a sequence or a graph via investigating temporal transitions of items in a session. However, these methods compress a session into one fixed representation vector without considering the target items to be predicted. The fixed vector will restrict the representation ability of the recommender model, considering the diversity of target items and users' interests. In this paper, we propose a novel target attentive graph neural network (TAGNN) model for session-based recommendation. In TAGNN, target-aware attention adaptively activates different user interests with respect to varied target items. The learned interest representation vector varies with different target items, greatly improving the expressiveness of the model. Moreover, TAGNN harnesses the power of graph neural networks to capture rich item transitions in sessions. Comprehensive experiments conducted on real-world datasets demonstrate its superiority over state-of-the-art methods.Comment: 5 pages, accepted to SIGIR 2020, authors' versio

Improving Molecular Pretraining with Complementary Featurizations

Molecular pretraining, which learns molecular representations over massive unlabeled data, has become a prominent paradigm to solve a variety of tasks in computational chemistry and drug discovery. Recently, prosperous progress has been made in molecular pretraining with different molecular featurizations, including 1D SMILES strings, 2D graphs, and 3D geometries. However, the role of molecular featurizations with their corresponding neural architectures in molecular pretraining remains largely unexamined. In this paper, through two case studies -- chirality classification and aromatic ring counting -- we first demonstrate that different featurization techniques convey chemical information differently. In light of this observation, we propose a simple and effective MOlecular pretraining framework with COmplementary featurizations (MOCO). MOCO comprehensively leverages multiple featurizations that complement each other and outperforms existing state-of-the-art models that solely relies on one or two featurizations on a wide range of molecular property prediction tasks.Comment: 24 pages, work in progres

Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis

Human brains lie at the core of complex neurobiological systems, where the neurons, circuits, and subsystems interact in enigmatic ways. Understanding the structural and functional mechanisms of the brain has long been an intriguing pursuit for neuroscience research and clinical disorder therapy. Mapping the connections of the human brain as a network is one of the most pervasive paradigms in neuroscience. Graph Neural Networks (GNNs) have recently emerged as a potential method for modeling complex network data. Deep models, on the other hand, have low interpretability, which prevents their usage in decision-critical contexts like healthcare. To bridge this gap, we propose an interpretable framework to analyze disorder-specific Regions of Interest (ROIs) and prominent connections. The proposed framework consists of two modules: a brain-network-oriented backbone model for disease prediction and a globally shared explanation generator that highlights disorder-specific biomarkers including salient ROIs and important connections. We conduct experiments on three real-world datasets of brain disorders. The results verify that our framework can obtain outstanding performance and also identify meaningful biomarkers. All code for this work is available at https://github.com/HennyJie/IBGNN.git.Comment: Previous version presented at icml-imlh 2021 (no proceedings, archived at 2107.05097), this version is accepted to miccai 202