MIRROR : Mining implicit relationships via structure-enhanced graph convolutional networks
- Authors: Liu, Jiaying , Xia, Feng , Ren, Jing , Xu, Bo , Pang, Guanson , Chi, Lianhua
- Date: 2023
- Type: Text , Journal article
- Relation: ACM Transactions on Knowledge Discovery from Data Vol. 17, no. 4 (2023), p.
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- Description: Data explosion in the information society drives people to develop more effective ways to extract meaningful information. Extracting semantic information and relational information has emerged as a key mining primitive in a wide variety of practical applications. Existing research on relation mining has primarily focused on explicit connections and ignored underlying information, e.g., the latent entity relations. Exploring such information (defined as implicit relationships in this article) provides an opportunity to reveal connotative knowledge and potential rules. In this article, we propose a novel research topic, i.e., how to identify implicit relationships across heterogeneous networks. Specially, we first give a clear and generic definition of implicit relationships. Then, we formalize the problem and propose an efficient solution, namely MIRROR, a graph convolutional network (GCN) model to infer implicit ties under explicit connections. MIRROR captures rich information in learning node-level representations by incorporating attributes from heterogeneous neighbors. Furthermore, MIRROR is tolerant of missing node attribute information because it is able to utilize network structure. We empirically evaluate MIRROR on four different genres of networks, achieving state-of-the-art performance for target relations mining. The underlying information revealed by MIRROR contributes to enriching existing knowledge and leading to novel domain insights. © 2023 Association for Computing Machinery.
MET-Meme : a multimodal meme dataset rich in metaphors
- Authors: Xu, Bo , Li, Tingtin , Zheng, Junzhe , Naseriparsa, Mehdi , Zhao, Zhehuan , Lin, Hongfei , Xia, Feng
- Date: 2022
- Type: Text , Conference paper
- Relation: 45th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, SIGIR 2022, Madrid, Spain, 11-15 July 2022, SIGIR 2022 - Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval p. 2887-2899
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- Description: Memes have become the popular means of communication for Internet users worldwide. Understanding the Internet meme is one of the most tricky challenges in natural language processing (NLP) tasks due to its convenient non-standard writing and network vocabulary. Recently, many linguists suggested that memes contain rich metaphorical information. However, the existing researches ignore this key feature. Therefore, to incorporate informative metaphors into the meme analysis, we introduce a novel multimodal meme dataset called MET-Meme, which is rich in metaphorical features. It contains 10045 text-image pairs, with manual annotations of the metaphor occurrence, sentiment categories, intentions, and offensiveness degree. Moreover, we propose a range of strong baselines to demonstrate the importance of combining metaphorical features for meme sentiment analysis and semantic understanding tasks, respectively. MET-Meme, and its code are released publicly for research in \urlhttps: //github.com/liaolianfoka/MET-Meme-A-Multi-modal-Meme-Dataset-Rich-in-Metaphors. © 2022 ACM.
Shifu2 : a network representation learning based model for advisor-advisee relationship mining
- Authors: Liu, Jiaying , Xia, Feng , Wang, Lei , Xu, Bo , Kong, Xiangjie
- Date: 2021
- Type: Text , Journal article
- Relation: IEEE Transactions on Knowledge and Data Engineering Vol. 33, no. 4 (2021), p. 1763-1777
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- Description: The advisor-advisee relationship represents direct knowledge heritage, and such relationship may not be readily available from academic libraries and search engines. This work aims to discover advisor-advisee relationships hidden behind scientific collaboration networks. For this purpose, we propose a novel model based on Network Representation Learning (NRL), namely Shifu2, which takes the collaboration network as input and the identified advisor-advisee relationship as output. In contrast to existing NRL models, Shifu2 considers not only the network structure but also the semantic information of nodes and edges. Shifu2 encodes nodes and edges into low-dimensional vectors respectively, both of which are then utilized to identify advisor-advisee relationships. Experimental results illustrate improved stability and effectiveness of the proposed model over state-of-the-art methods. In addition, we generate a large-scale academic genealogy dataset by taking advantage of Shifu2. © 1989-2012 IEEE.
Graph Force Learning
- Authors: Sun, Ke , Liu, Jiaying , Yu, Shuo , Xu, Bo , Xia, Feng
- Date: 2020
- Type: Text , Conference paper
- Relation: 8th IEEE International Conference on Big Data, Big Data 2020 p. 2987-2994
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- Description: Features representation leverages the great power in network analysis tasks. However, most features are discrete which poses tremendous challenges to effective use. Recently, increasing attention has been paid on network feature learning, which could map discrete features to continued space. Unfortunately, current studies fail to fully preserve the structural information in the feature space due to random negative sampling strategy during training. To tackle this problem, we study the problem of feature learning and novelty propose a force-based graph learning model named GForce inspired by the spring-electrical model. GForce assumes that nodes are in attractive forces and repulsive forces, thus leading to the same representation with the original structural information in feature learning. Comprehensive experiments on three benchmark datasets demonstrate the effectiveness of the proposed framework. Furthermore, GForce opens up opportunities to use physics models to model node interaction for graph learning. © 2020 IEEE.
MODEL : motif-based deep feature learning for link prediction
- Authors: Wang, Lei , Ren, Jing , Xu, Bo , Li, Jianxin , Luo, Wei , Xia, Feng
- Date: 2020
- Type: Text , Journal article
- Relation: IEEE Transactions on Computational Social Systems Vol. 7, no. 2 (2020), p. 503-516
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- Description: Link prediction plays an important role in network analysis and applications. Recently, approaches for link prediction have evolved from traditional similarity-based algorithms into embedding-based algorithms. However, most existing approaches fail to exploit the fact that real-world networks are different from random networks. In particular, real-world networks are known to contain motifs, natural network building blocks reflecting the underlying network-generating processes. In this article, we propose a novel embedding algorithm that incorporates network motifs to capture higher order structures in the network. To evaluate its effectiveness for link prediction, experiments were conducted on three types of networks: social networks, biological networks, and academic networks. The results demonstrate that our algorithm outperforms both the traditional similarity-based algorithms (by 20%) and the state-of-the-art embedding-based algorithms (by 19%). © 2014 IEEE.
Motif discovery in networks : a survey
- Authors: Yu, Shuo , Feng, Yufan , Zhang, Da , Bedru, Hayat , Xu, Bo , Xia, Feng
- Date: 2020
- Type: Text , Journal article
- Relation: Computer Science Review Vol. 37, no. (2020), p.
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- Description: Motifs are regarded as network blocks because motifs can be used to present fundamental patterns in networks. Motif discovery is well applied in various scientific problems, including subgraph mining and graph isomorphism tasks. This paper analyzes and summarizes current motif discovery algorithms in the field of network science with both efficiency and accuracy perspectives. In this paper, we present motif discovery algorithms, including MFinder, FanMod, Grochow, MODA, Kavosh, G-tries, QuateXelero, color-coding approaches, and GPU-based approaches. Based on that, we discuss the real-world applications of the algorithms mentioned above under different scenarios. Since motif discovery algorithms are diffusely demanded in many applications, several challenges may be firstly handled, including high computational complexity, higher order motif discovery, same motif detection, discovering heterogeneous sizes of motifs, as well as motif discovery results visualization. This work sheds light on current research progress and future research orientations. © 2020 Elsevier Inc.
Network representation learning: From traditional feature learning to deep learning
- Authors: Sun, Ke , Wang, Lei , Xu, Bo , Zhao, Wenhong , Teng, Shyh , Xia, Feng
- Date: 2020
- Type: Text , Journal article
- Relation: IEEE Access Vol. 8, no. (2020), p. 205600-205617
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- Description: Network representation learning (NRL) is an effective graph analytics technique and promotes users to deeply understand the hidden characteristics of graph data. It has been successfully applied in many real-world tasks related to network science, such as social network data processing, biological information processing, and recommender systems. Deep Learning is a powerful tool to learn data features. However, it is non-trivial to generalize deep learning to graph-structured data since it is different from the regular data such as pictures having spatial information and sounds having temporal information. Recently, researchers proposed many deep learning-based methods in the area of NRL. In this survey, we investigate classical NRL from traditional feature learning method to the deep learning-based model, analyze relationships between them, and summarize the latest progress. Finally, we discuss open issues considering NRL and point out the future directions in this field. © 2020 Institute of Electrical and Electronics Engineers Inc.. All rights reserved.
DINE : a framework for deep incomplete network embedding
- Authors: Hou, Ke , Liu, Jiaying , Peng, Yin , Xu, Bo , Lee, Ivan , Xia, Feng
- Date: 2019
- Type: Text , Conference paper
- Relation: 32nd Australasian Joint Conference on Artificial Intelligence, AI 2019 Vol. 11919 LNAI, p. 165-176
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- Description: Network representation learning (NRL) plays a vital role in a variety of tasks such as node classification and link prediction. It aims to learn low-dimensional vector representations for nodes based on network structures or node attributes. While embedding techniques on complete networks have been intensively studied, in real-world applications, it is still a challenging task to collect complete networks. To bridge the gap, in this paper, we propose a Deep Incomplete Network Embedding method, namely DINE. Specifically, we first complete the missing part including both nodes and edges in a partially observable network by using the expectation-maximization framework. To improve the embedding performance, we consider both network structures and node attributes to learn node representations. Empirically, we evaluate DINE over three networks on multi-label classification and link prediction tasks. The results demonstrate the superiority of our proposed approach compared against state-of-the-art baselines. © 2019, Springer Nature Switzerland AG.
- Description: E1
Disease gene prediction based on heterogeneous probabilistic hypergraph ranking
- Authors: Ding, Feng , Kong, Xiangjie , Zhao, Zhehuan , Xia, Feng , Liu, Anfu , Bai, Chenxu , Xu, Bo , Liu, Xiaoxia , Sang, Shengtian , Lin, Hongfei , Yang, Zhihao , Wang, Jian
- Date: 2019
- Type: Text , Conference proceedings
- Relation: 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); San Diego, CA, USA; 18-21 November 2019 p. 2021-2028
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- Description: In order to save time and cost, many disease gene prediction methods have been proposed in recent years. However, the traditional network model uses a binary relationship to represent the relationship between different proteins or gene molecules and phenotypes, which leads to the loss of information. Recently, hypergraph shows that it can overcome this loss of information to some extent and preserve the multivariate relationship, so we transformed the disease gene prediction problem into the problem of ranking the multivariate-relationship object. In this paper, we propose a method of Heterogeneous Probabilistic Hypergraph Ranking (HPHR) to predict disease genes. Firstly, fix a graph centroid for each hyperedge and according to different associations, and add other nodes related to the graph centroid to hyperedges with a certain probability. Then transform the problem of predicting disease genes into the problem of ranking heterogeneous objects, and the candidate genes are sorted by hypergraph ranking. The method is then applied to the integrated disease gene network. Compared with other prediction methods achieved better results, which was verified by this experiment.
Protein complexes detection based on global network representation learning
- Authors: Xu, Bo , Li, Kun , Liu, Xiaoxia , Liu, Delong , Zhang, Yijia , Lin, Hongfei , Yang, Zhihao , Wang, Jian , Xia, Feng
- Date: 2018
- Type: Text , Conference proceedings
- Relation: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); Madrid, Spain; 3-6 Dec. 2018 p. 210-213
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- Description: Detecting protein complexes from protein-protein interaction (PPI) networks allows biologists reveal the principle of cellular organization and functions. Existing computational methods try to incorporate biological evidence to enhance the quality of predicted complexes. However, it is still a challenge to integrate biological information into complexes discovery process under a unified framework. Recently, network embedding methods showed their effectiveness in graph data analysis tasks. It provides a framework for incorporating both network structure and additional node attribute information. This salient feature is particularly desirable in the context of protein complexes identification. However, none of the existing network embedding methods take node attribute proximity and high-order structure proximity into account at the same time. In this paper, we propose a novel global network embedding method, which preserves global network structure and biological information. We utilize this global representation learning method to learn vector representation for proteins. Then, we use a seed-extension clustering method to discover overlapping protein complexes with the embedding results. This novel protein complexes detection method we called GLONE. Evaluated on five real yeast PPI networks, our method outperforms the competing algorithms in terms of different evaluation metrics.