Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction.
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IFIP TC13 Conference on Human-Computer Interaction是人機交互領域的研究者和實踐者展示其工作的重要平臺。多年來，這些會議吸引了來自幾個國家和文化的研究人員。官網鏈接： ·
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Training deep neural network (DNN) models, which has become an important task in today's software development, is often costly in terms of computational resources and time. With the inspiration of software reuse, building DNN models through reusing existing ones has gained increasing attention recently. Prior approaches to DNN model reuse have two main limitations: 1) reusing the entire model, while only a small part of the model's functionalities (labels) are required, would cause much overhead (e.g., computational and time costs for inference), and 2) model reuse would inherit the defects and weaknesses of the reused model, and hence put the new system under threats of security attack. To solve the above problem, we propose SeaM, a tool that re-engineers a trained DNN model to improve its reusability. Specifically, given a target problem and a trained model, SeaM utilizes a gradient-based search method to search for the model's weights that are relevant to the target problem. The re-engineered model that only retains the relevant weights is then reused to solve the target problem. Evaluation results on widely-used models show that the re-engineered models produced by SeaM only contain 10.11% weights of the original models, resulting 42.41% reduction in terms of inference time. For the target problem, the re-engineered models even outperform the original models in classification accuracy by 5.85%. Moreover, reusing the re-engineered models inherits an average of 57% fewer defects than reusing the entire model. We believe our approach to reducing reuse overhead and defect inheritance is one important step forward for practical model reuse.
Graph mining tasks arise from many different application domains, ranging from social networks, transportation, E-commerce, etc., which have been receiving great attention from the theoretical and algorithm design communities in recent years, and there has been some pioneering work using the hotly researched reinforcement learning (RL) techniques to address graph data mining tasks. However, these graph mining algorithms and RL models are dispersed in different research areas, which makes it hard to compare different algorithms with each other. In this survey, we provide a comprehensive overview of RL models and graph mining and generalize these algorithms to Graph Reinforcement Learning (GRL) as a unified formulation. We further discuss the applications of GRL methods across various domains and summarize the method description, open-source codes, and benchmark datasets of GRL methods. Finally, we propose possible important directions and challenges to be solved in the future. This is the latest work on a comprehensive survey of GRL literature, and this work provides a global view for researchers as well as a learning resource for researchers outside the domain. In addition, we create an online open-source for both interested researchers who want to enter this rapidly developing domain and experts who would like to compare GRL methods.
Deep learning techniques have led to remarkable breakthroughs in the field of generic object detection and have spawned a lot of scene-understanding tasks in recent years. Scene graph has been the focus of research because of its powerful semantic representation and applications to scene understanding. Scene Graph Generation (SGG) refers to the task of automatically mapping an image into a semantic structural scene graph, which requires the correct labeling of detected objects and their relationships. Although this is a challenging task, the community has proposed a lot of SGG approaches and achieved good results. In this paper, we provide a comprehensive survey of recent achievements in this field brought about by deep learning techniques. We review 138 representative works that cover different input modalities, and systematically summarize existing methods of image-based SGG from the perspective of feature extraction and fusion. We attempt to connect and systematize the existing visual relationship detection methods, to summarize, and interpret the mechanisms and the strategies of SGG in a comprehensive way. Finally, we finish this survey with deep discussions about current existing problems and future research directions. This survey will help readers to develop a better understanding of the current research status and ideas.
A community reveals the features and connections of its members that are different from those in other communities in a network. Detecting communities is of great significance in network analysis. Despite the classical spectral clustering and statistical inference methods, we notice a significant development of deep learning techniques for community detection in recent years with their advantages in handling high dimensional network data. Hence, a comprehensive overview of community detection's latest progress through deep learning is timely to both academics and practitioners. This survey devises and proposes a new taxonomy covering different categories of the state-of-the-art methods, including deep learning-based models upon deep neural networks, deep nonnegative matrix factorization and deep sparse filtering. The main category, i.e., deep neural networks, is further divided into convolutional networks, graph attention networks, generative adversarial networks and autoencoders. The survey also summarizes the popular benchmark data sets, model evaluation metrics, and open-source implementations to address experimentation settings. We then discuss the practical applications of community detection in various domains and point to implementation scenarios. Finally, we outline future directions by suggesting challenging topics in this fast-growing deep learning field.
Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction, MIRACLE for brevity, to capture inter-view molecule structure and intra-view interactions between molecules simultaneously. MIRACLE treats a DDI network as a multi-view graph where each node in the interaction graph itself is a drug molecular graph instance. We use GCNs and bond-aware attentive message passing networks to encode DDI relationships and drug molecular graphs in the MIRACLE learning stage, respectively. Also, we propose a novel unsupervised contrastive learning component to balance and integrate the multi-view information. Comprehensive experiments on multiple real datasets show that MIRACLE outperforms the state-of-the-art DDI prediction models consistently.
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.
The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.
Transfer learning aims at improving the performance of target learners on target domains by transferring the knowledge contained in different but related source domains. In this way, the dependence on a large number of target domain data can be reduced for constructing target learners. Due to the wide application prospects, transfer learning has become a popular and promising area in machine learning. Although there are already some valuable and impressive surveys on transfer learning, these surveys introduce approaches in a relatively isolated way and lack the recent advances in transfer learning. As the rapid expansion of the transfer learning area, it is both necessary and challenging to comprehensively review the relevant studies. This survey attempts to connect and systematize the existing transfer learning researches, as well as to summarize and interpret the mechanisms and the strategies in a comprehensive way, which may help readers have a better understanding of the current research status and ideas. Different from previous surveys, this survey paper reviews over forty representative transfer learning approaches from the perspectives of data and model. The applications of transfer learning are also briefly introduced. In order to show the performance of different transfer learning models, twenty representative transfer learning models are used for experiments. The models are performed on three different datasets, i.e., Amazon Reviews, Reuters-21578, and Office-31. And the experimental results demonstrate the importance of selecting appropriate transfer learning models for different applications in practice.
Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into different categories. With a focus on graph convolutional networks, we review alternative architectures that have recently been developed; these learning paradigms include graph attention networks, graph autoencoders, graph generative networks, and graph spatial-temporal networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes and benchmarks of the existing algorithms on different learning tasks. Finally, we propose potential research directions in this fast-growing field.
Deep learning has been shown successful in a number of domains, ranging from acoustics, images to natural language processing. However, applying deep learning to the ubiquitous graph data is non-trivial because of the unique characteristics of graphs. Recently, a significant amount of research efforts have been devoted to this area, greatly advancing graph analyzing techniques. In this survey, we comprehensively review different kinds of deep learning methods applied to graphs. We divide existing methods into three main categories: semi-supervised methods including Graph Neural Networks and Graph Convolutional Networks, unsupervised methods including Graph Autoencoders, and recent advancements including Graph Recurrent Neural Networks and Graph Reinforcement Learning. We then provide a comprehensive overview of these methods in a systematic manner following their history of developments. We also analyze the differences of these methods and how to composite different architectures. Finally, we briefly outline their applications and discuss potential future directions.
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