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1. A Differential Geometric View and Explainability of GNN on Evolving Graphs

   Liu, Yazheng Liu ; Zhang, Xi ; Xie, Sihong ( May 2023 , The Eleventh International Conference on Learning Representations (ICLR 2023))

   Graphs are ubiquitous in social networks and biochemistry, where Graph Neural Networks (GNN) are the state-of-the-art models for prediction. Graphs can be evolving and it is vital to formally model and understand how a trained GNN responds to graph evolution. We propose a smooth parameterization of the GNN predicted distributions using axiomatic attribution, where the distributions are on a low-dimensional manifold within a high-dimensional embedding space. We exploit the differential geometric viewpoint to model distributional evolution as smooth curves on the manifold. We reparameterize families of curves on the manifold and design a convex optimization problem to find a unique curve that concisely approximates the distributional evolution for human interpretation. Extensive experiments on node classification, link prediction, and graph classification tasks with evolving graphs demonstrate the better sparsity, faithfulness, and intuitiveness of the proposed method over the state-of-the-art methods. 

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2. Strategies For Pre-training Graph Neural Networks

   Hu, W. ; Liu, B. ; Gomes, J. ; Zitnik, M. ; Liang, P. ; Pande, V. ; Leskovec, J. ( April 2020 , International Conference on Learning Representations (ICLR))

   Many applications of machine learning require a model to make accurate predictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naïve strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction. 

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3. Predicting ncRNA–protein interactions based on dual graph convolutional network and pairwise learning

   https://doi.org/10.1093/bib/bbac339  

   Zhuo, Linlin ; song, bosheng ; liu, yuansheng ; Li, Zejun ; Fu, Xiangzheng ( September 2022 , Briefings in Bioinformatics)

   Noncoding RNAs (ncRNAs) have recently attracted considerable attention due to their key roles in biology. The ncRNA–proteins interaction (NPI) is often explored to reveal some biological activities that ncRNA may affect, such as biological traits, diseases, etc. Traditional experimental methods can accomplish this work but are often labor-intensive and expensive. Machine learning and deep learning methods have achieved great success by exploiting sufficient sequence or structure information. Graph Neural Network (GNN)-based methods consider the topology in ncRNA–protein graphs and perform well on tasks like NPI prediction. Based on GNN, some pairwise constraint methods have been developed to apply on homogeneous networks, but not used for NPI prediction on heterogeneous networks. In this paper, we construct a pairwise constrained NPI predictor based on dual Graph Convolutional Network (GCN) called NPI-DGCN. To our knowledge, our method is the first to train a heterogeneous graph-based model using a pairwise learning strategy. Instead of binary classification, we use a rank layer to calculate the score of an ncRNA–protein pair. Moreover, our model is the first to predict NPIs on the ncRNA–protein bipartite graph rather than the homogeneous graph. We transform the original ncRNA–protein bipartite graph into two homogenous graphs on which to explore second-order implicit relationships. At the same time, we model direct interactions between two homogenous graphs to explore explicit relationships. Experimental results on the four standard datasets indicate that our method achieves competitive performance with other state-of-the-art methods. And the model is available at https://github.com/zhuoninnin1992/NPIPredict

    

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4. DyRep: Learning Representations over Dynamic Graphs

   Trivedi, Rakshit ; Farajtabar, Mehrdad ; Biswal, Prasenjeet ; Zha, Hongyuan ( May 2019 , International Conference on Learning Representations)

   Representation Learning over graph structured data has received significant attention recently due to its ubiquitous applicability. However, most advancements have been made in static graph settings while efforts for jointly learning dynamic of the graph and dynamic on the graph are still in an infant stage. Two fundamental questions arise in learning over dynamic graphs: (i) How to elegantly model dynamical processes over graphs? (ii) How to leverage such a model to effectively encode evolving graph information into low-dimensional representations? We present DyRep - a novel modeling framework for dynamic graphs that posits representation learning as a latent mediation process bridging two observed processes namely -- dynamics of the network (realized as topological evolution) and dynamics on the network (realized as activities between nodes). Concretely, we propose a two-time scale deep temporal point process model that captures the interleaved dynamics of the observed processes. This model is further parameterized by a temporal-attentive representation network that encodes temporally evolving structural information into node representations which in turn drives the nonlinear evolution of the observed graph dynamics. Our unified framework is trained using an efficient unsupervised procedure and has capability to generalize over unseen nodes. We demonstrate that DyRep outperforms state-of-the-art baselines for dynamic link prediction and time prediction tasks and present extensive qualitative insights into our framework. 

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5. DYREP: Learning Representations Over Dynamic Graphs

   Trivedi, Rakshit ; Farajtabar, Mehrdad ; Biswal, Prasenjeet ; Zha, Hongyuan ( January 2019 , International Conference on Learning Representation)

   Representation Learning over graph structured data has received significant attention recently due to its ubiquitous applicability. However, most advancements have been made in static graph settings while efforts for jointly learning dynamic of the graph and dynamic on the graph are still in an infant stage. Two fundamental questions arise in learning over dynamic graphs: (i) How to elegantly model dynamical processes over graphs? (ii) How to leverage such a model to effectively encode evolving graph information into low-dimensional representations? We present DyRep - a novel modeling framework for dynamic graphs that posits representation learning as a latent mediation process bridging two observed processes namely – dynamics of the network (realized as topological evolution) and dynamics on the network (realized as activities between nodes). Concretely, we propose a two-time scale deep temporal point process model that captures the interleaved dynamics of the observed processes. This model is further parameterized by a temporal-attentive representation network that encodes temporally evolving structural information into node representations which in turn drives the nonlinear evolution of the observed graph dynamics. Our unified framework is trained using an efficient unsupervised procedure and has capability to generalize over unseen nodes. We demonstrate that DyRep outperforms state-of-the-art baselines for dynamic link prediction and time prediction tasks and present extensive qualitative insights into our framework. 

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