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1. Product Competition Prediction in Engineering Design Using Graph Neural Networks

   https://doi.org/10.1115/1.4054299  

   Ahmed, Faez; Cui, Yaxin; Fu, Yan; Chen, Wei (January 2022, ASME Open Journal of Engineering)

   Abstract Understanding relationships between different products in a market system and predicting how changes in design impact their market position can be instrumental for companies to create better products. We propose a graph neural network-based method for modeling relationships between products, where nodes in a network represent products and edges represent their relationships. Our modeling enables a systematic way to predict the relationship links between unseen products for future years. When applied to a Chinese car market case study, our method based on an inductive graph neural network approach, GraphSAGE, yields double the link prediction performance compared to an existing network modeling method—exponential random graph model-based method for predicting the car co-consideration relationships. Our work also overcomes scalability and multiple data type-related limitations of the traditional network modeling methods by modeling a larger number of attributes, mixed categorical and numerical attributes, and unseen products. While a vanilla GraphSAGE requires a partial network to make predictions, we augment it with an “adjacency prediction model” to circumvent the limitation of needing neighborhood information. Finally, we demonstrate how insights obtained from a permutation-based interpretability analysis can help a manufacturer understand how design attributes impact the predictions of product relationships. Overall, this work provides a systematic data-driven method to predict the relationships between products in a complex network such as the car market. 

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2. Edgeformers: Graph-Empowered Transformers for Representation Learning on Textual-Edge Networks

   Jin, Bowen; Zhang, Yu; Meng, Yu; Han, Jiawei (May 2023, The Eleventh International Conference on Learning Representations, {ICLR} 2023)

   Edges in many real-world social/information networks are associated with rich text information (e.g., user-user communications or user-product reviews). However, mainstream network representation learning models focus on propagating and aggregating node attributes, lacking specific designs to utilize text semantics on edges. While there exist edge-aware graph neural networks, they directly initialize edge attributes as a feature vector, which cannot fully capture the contextualized text semantics of edges. In this paper, we propose Edgeformers, a framework built upon graph-enhanced Transformers, to perform edge and node representation learning by modeling texts on edges in a contextualized way. Specifically, in edge representation learning, we inject network information into each Transformer layer when encoding edge texts; in node representation learning, we aggregate edge representations through an attention mechanism within each node’s ego-graph. On five public datasets from three different domains, Edgeformers consistently outperform state-of-the-art baselines in edge classification and link prediction, demonstrating the efficacy in learning edge and node representations, respectively. 

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3. Supervised Graph Representation Learning for Modeling the Relationship between Structural and Functional Brain Connectivity

   https://doi.org/10.1109/ICASSP40776.2020.9053711  

   Li, Yang; Shafipour, Rasoul; Mateos, Gonzalo; Zhang, Zhengwu (May 2020, 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP))

   null (Ed.)

   In this paper, we propose a supervised graph representation learning method to model the relationship between brain functional connectivity (FC) and structural connectivity (SC) through a graph encoder-decoder system. The graph convolutional network (GCN) model is leveraged in the encoder to learn lower-dimensional node representations (i.e. node embeddings) integrating information from both node attributes and network topology. In doing so, the encoder manages to capture both direct and indirect interactions between brain regions in the node embeddings which later help reconstruct empirical FC networks. From node embeddings, graph representations are learnt to embed the entire graphs into a vector space. Our end-to-end model utilizes a multi-objective loss function to simultaneously learn node representations for FC network reconstruction and graph representations for subject classification. The experiment on a large population of non-drinkers and heavy drinkers shows that our model can provide a characterization of the population pattern in the SC-FC relationship, while also learning features that capture individual uniqueness for subject classification. The identified key brain subnetworks show significant between-group difference and support the promising prospect of GCN-based graph representation learning on brain networks to model human brain activity and function. 

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4. Dynamic Relevance Graph Network for Knowledge-Aware Question Answering

   Zheng, Chen; Kordjamshidi, Parisa (October 2022, Proceedings of the 29th International Conference on Computational Linguistics)

   This work investigates the challenge of learning and reasoning for Commonsense Question Answering given an external source of knowledge in the form of a knowledge graph (KG). We propose a novel graph neural network architecture, called Dynamic Relevance Graph Network (DRGN). DRGN operates on a given KG subgraph based on the question and answers entities and uses the relevance scores between the nodes to establish new edges dynamically for learning node representations in the graph network. This explicit usage of relevance as graph edges has the following advantages, a) the model can exploit the existing relationships, re-scale the node weights, and influence the way the neighborhood nodes’ representations are aggregated in the KG subgraph, b) It potentially recovers the missing edges in KG that are needed for reasoning. Moreover, as a byproduct, our model improves handling the negative questions due to considering the relevance between the question node and the graph entities. Our proposed approach shows competitive performance on two QA benchmarks, CommonsenseQA and OpenbookQA, compared to the state-of-the-art published results. 

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5. Learning graph representations of biochemical networks and its application to enzymatic link prediction

   https://doi.org/10.1093/bioinformatics/btaa881  

   Jiang, Julie; Liu, Li-Ping; Hassoun, Soha (October 2020, Bioinformatics)

   Martelli, Pier Luigi (Ed.)

   Abstract Motivation The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity. Results We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization. Availability and implementation The code and datasets are available through https://github.com/HassounLab/ELP. 

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