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Graph-based neural network models are gaining traction in the field of representation learning due to their ability to uncover latent topological relationships between entities that are otherwise challenging to identify. These models have been employed across a diverse range of domains, encompassing drug discovery, protein interactions, semantic segmentation, and fluid dynamics research. In this study, we investigate the potential of Graph Neural Networks (GNNs) for medical image classification. We introduce a novel model that combines GNNs and edge convolution, leveraging the interconnectedness of RGB channel feature values to strongly represent connections between crucial graph nodes. Our proposed model not only performs on par with state-of-the-art Deep Neural Networks (DNNs) but does so with 1000 times fewer parameters, resulting in reduced training time and data requirements. We compare our Graph Convolutional Neural Network (GCNN) to pre-trained DNNs for classifying MedMNIST dataset classes, revealing promising prospects for GNNs in medical image analysis. Our results also encourage further exploration of advanced graph-based models such as Graph Attention Networks (GAT) and Graph Auto-Encoders in the medical imaging domain. The proposed model yields more reliable, interpretable, and accurate outcomes for tasks like semantic segmentation and image classification compared to simpler GCNNs

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Text Classification is the most essential and fundamental problem in Natural Language Processing. While numerous recent text classification models applied the sequential deep learning technique, graph neural network-based models can directly deal with complex structured text data and exploit global information. Many real text classification applications can be naturally cast into a graph, which captures words, documents, and corpus global features. In this survey, we bring the coverage of methods up to 2023, including corpus-level and document-level graph neural networks. We discuss each of these methods in detail, dealing with the graph construction mechanisms and the graph-based learning process. As well as the technological survey, we look at issues behind and future directions addressed in text classification using graph neural networks. We also cover datasets, evaluation metrics, and experiment design and present a summary of published performance on the publicly available benchmarks. Note that we present a comprehensive comparison between different techniques and identify the pros and cons of various evaluation metrics in this survey.

Deep learning has become the dominant approach in coping with various tasks in Natural LanguageProcessing (NLP). Although text inputs are typically represented as a sequence of tokens, there isa rich variety of NLP problems that can be best expressed with a graph structure. As a result, thereis a surge of interests in developing new deep learning techniques on graphs for a large numberof NLP tasks. In this survey, we present a comprehensive overview onGraph Neural Networks(GNNs) for Natural Language Processing. We propose a new taxonomy of GNNs for NLP, whichsystematically organizes existing research of GNNs for NLP along three axes: graph construction,graph representation learning, and graph based encoder-decoder models. We further introducea large number of NLP applications that are exploiting the power of GNNs and summarize thecorresponding benchmark datasets, evaluation metrics, and open-source codes. Finally, we discussvarious outstanding challenges for making the full use of GNNs for NLP as well as future researchdirections. To the best of our knowledge, this is the first comprehensive overview of Graph NeuralNetworks for Natural Language Processing.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.

Pre-training text representations has recently been shown to significantly improve the state-of-the-art in many natural language processing tasks. The central goal of pre-training is to learn text representations that are useful for subsequent tasks. However, existing approaches are optimized by minimizing a proxy objective, such as the negative log likelihood of language modeling. In this work, we introduce a learning algorithm which directly optimizes model's ability to learn text representations for effective learning of downstream tasks. We show that there is an intrinsic connection between multi-task pre-training and model-agnostic meta-learning with a sequence of meta-train steps. The standard multi-task learning objective adopted in BERT is a special case of our learning algorithm where the depth of meta-train is zero. We study the problem in two settings: unsupervised pre-training and supervised pre-training with different pre-training objects to verify the generality of our approach.Experimental results show that our algorithm brings improvements and learns better initializations for a variety of downstream tasks.

Reasoning with knowledge expressed in natural language and Knowledge Bases (KBs) is a major challenge for Artificial Intelligence, with applications in machine reading, dialogue, and question answering. General neural architectures that jointly learn representations and transformations of text are very data-inefficient, and it is hard to analyse their reasoning process. These issues are addressed by end-to-end differentiable reasoning systems such as Neural Theorem Provers (NTPs), although they can only be used with small-scale symbolic KBs. In this paper we first propose Greedy NTPs (GNTPs), an extension to NTPs addressing their complexity and scalability limitations, thus making them applicable to real-world datasets. This result is achieved by dynamically constructing the computation graph of NTPs and including only the most promising proof paths during inference, thus obtaining orders of magnitude more efficient models. Then, we propose a novel approach for jointly reasoning over KBs and textual mentions, by embedding logic facts and natural language sentences in a shared embedding space. We show that GNTPs perform on par with NTPs at a fraction of their cost while achieving competitive link prediction results on large datasets, providing explanations for predictions, and inducing interpretable models. Source code, datasets, and supplementary material are available online at //github.com/uclnlp/gntp.

Language model pre-training has proven to be useful in learning universal language representations. As a state-of-the-art language model pre-training model, BERT (Bidirectional Encoder Representations from Transformers) has achieved amazing results in many language understanding tasks. In this paper, we conduct exhaustive experiments to investigate different fine-tuning methods of BERT on text classification task and provide a general solution for BERT fine-tuning. Finally, the proposed solution obtains new state-of-the-art results on eight widely-studied text classification datasets.

Graph convolutional networks (GCNs) have been successfully applied in node classification tasks of network mining. However, most of these models based on neighborhood aggregation are usually shallow and lack the "graph pooling" mechanism, which prevents the model from obtaining adequate global information. In order to increase the receptive field, we propose a novel deep Hierarchical Graph Convolutional Network (H-GCN) for semi-supervised node classification. H-GCN first repeatedly aggregates structurally similar nodes to hyper-nodes and then refines the coarsened graph to the original to restore the representation for each node. Instead of merely aggregating one- or two-hop neighborhood information, the proposed coarsening procedure enlarges the receptive field for each node, hence more global information can be learned. Comprehensive experiments conducted on public datasets demonstrate the effectiveness of the proposed method over the state-of-art methods. Notably, our model gains substantial improvements when only a few labeled samples are provided.