Xiao-Li Li

Ziyang Wang, Wei Wei, Gao Cong et al.

Session-based recommendation (SBR) is a challenging task, which aims at recommending items based on anonymous behavior sequences. Almost all the existing solutions for SBR model user preference only based on the current session without exploiting the other sessions, which may contain both relevant and irrelevant item-transitions to the current session. This paper proposes a novel approach, called Global Context Enhanced Graph Neural Networks (GCE-GNN) to exploit item transitions over all sessions in a more subtle manner for better inferring the user preference of the current session. Specifically, GCE-GNN learns two levels of item embeddings from session graph and global graph, respectively: (i) Session graph, which is to learn the session-level item embedding by modeling pairwise item-transitions within the current session; and (ii) Global graph, which is to learn the global-level item embedding by modeling pairwise item-transitions over all sessions. In GCE-GNN, we propose a novel global-level item representation learning layer, which employs a session-aware attention mechanism to recursively incorporate the neighbors' embeddings of each node on the global graph. We also design a session-level item representation learning layer, which employs a GNN on the session graph to learn session-level item embeddings within the current session. Moreover, GCE-GNN aggregates the learnt item representations in the two levels with a soft attention mechanism. Experiments on three benchmark datasets demonstrate that GCE-GNN outperforms the state-of-the-art methods consistently.

Ziyang Wang, Wei Wei, Xian-Ling Mao et al.

Session-based recommendation (SBR) is a challenging task, which aims to predict users' future interests based on anonymous behavior sequences. Existing methods leverage powerful representation learning approaches to encode sessions into a low-dimensional space. However, despite such achievements, all the existing studies focus on the instance-level session learning, while neglecting the group-level users' preference, which is significant to model the users' behavior. To this end, we propose a novel Repeat-aware Neural Mechanism for Session-based Recommendation (RNMSR). In RNMSR, we propose to learn the user preference from both instance-level and group-level, respectively: (i) instance-level, which employs GNNs on a similarity-based item-pairwise session graph to capture the users' preference in instance-level. (ii) group-level, which converts sessions into group-level behavior patterns to model the group-level users' preference. In RNMSR, we combine instance-level user preference and group-level user preference to model the repeat consumption of users, \ie whether users take repeated consumption and which items are preferred by users. Extensive experiments are conducted on three real-world datasets, \ie Diginetica, Yoochoose, and Nowplaying, demonstrating that the proposed method consistently achieves state-of-the-art performance in all the tests.

Ziyang Wang, Wei Wei, Gao Cong et al.

Session-based recommendation (SBR) is a challenging task, which aims at recommending items based on anonymous behavior sequences. Most existing SBR studies model the user preferences based only on the current session while neglecting the item-transition information from the other sessions, which suffer from the inability of modeling the complicated item-transition pattern. To address the limitations, we introduce global item-transition information to strength the modeling of the dynamic item-transition. For fully exploiting the global item-transition information, two ways of exploring global information for SBR are studied in this work. Specifically, we first propose a basic GNN-based framework (BGNN), which solely uses session-level item-transition information on session graph. Based on BGNN, we propose a novel approach, called Session-based Recommendation with Global Information (SRGI), which infers the user preferences via fully exploring global item-transitions over all sessions from two different perspectives: (i) Fusion-based Model (SRGI-FM), which recursively incorporates the neighbor embeddings of each node on global graph into the learning process of session level item representation; and (ii) Constrained-based Model (SRGI-CM), which treats the global-level item-transition information as a constraint to ensure the learned item embeddings are consistent with the global item-transition. Extensive experiments conducted on three popular benchmark datasets demonstrate that both SRGI-FM and SRGI-CM outperform the state-of-the-art methods consistently.

Sezin Kircali Ata, Min Wu, Yuan Fang et al.

Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations. Considering the huge number of possible mutations, in addition to its high cost, another important drawback of GWAS analysis is the large number of false-positives. Thus, researchers search for more evidence to cross-check their results through different sources. To provide the researchers with alternative low-cost disease-gene association evidence, computational approaches come into play. Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction. In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods. To summarize, we first elucidate the task definition for disease gene prediction. Secondly, we categorize existing network-based efforts into network diffusion methods, traditional machine learning methods with handcrafted graph features and graph representation learning methods. Thirdly, an empirical analysis is conducted to evaluate the performance of the selected methods across seven diseases. We also provide distinguishing findings about the discussed methods based on our empirical analysis. Finally, we highlight potential research directions for future studies on disease gene prediction.

Yong Liu, Min Wu, Chenghao Liu et al.

Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell lines. Therefore, computational prediction methods are needed to address these issues. This paper proposes a novel SL prediction method, named SL2MF, which employs logistic matrix factorization to learn latent representations of genes from the observed SL data. The probability that two genes are likely to form SL is modeled by the linear combination of gene latent vectors. As known SL pairs are more trustworthy than unknown pairs, we design importance weighting schemes to assign higher importance weights for known SL pairs and lower importance weights for unknown pairs in SL2MF. Moreover, we also incorporate biological knowledge about genes from protein-protein interaction (PPI) data and Gene Ontology (GO). In particular, we calculate the similarity between genes based on their GO annotations and topological properties in the PPI network. Extensive experiments on the SL interaction data from SynLethDB database have been conducted to demonstrate the effectiveness of SL2MF.

Bo Zhang, Wei Li, Jie Hao et al.

Traditional intelligent fault diagnosis of rolling bearings work well only under a common assumption that the labeled training data (source domain) and unlabeled testing data (target domain) are drawn from the same distribution. However, in many real-world applications, this assumption does not hold, especially when the working condition varies. In this paper, a new adversarial adaptive 1-D CNN called A2CNN is proposed to address this problem. A2CNN consists of four parts, namely, a source feature extractor, a target feature extractor, a label classifier and a domain discriminator. The layers between the source and target feature extractor are partially untied during the training stage to take both training efficiency and domain adaptation into consideration. Experiments show that A2CNN has strong fault-discriminative and domain-invariant capacity, and therefore can achieve high accuracy under different working conditions. We also visualize the learned features and the networks to explore the reasons behind the high performance of our proposed model.

Sujatha Das Gollapalli, Xiao-li Li

Keyphrases efficiently summarize a document's content and are used in various document processing and retrieval tasks. Several unsupervised techniques and classifiers exist for extracting keyphrases from text documents. Most of these methods operate at a phrase-level and rely on part-of-speech (POS) filters for candidate phrase generation. In addition, they do not directly handle keyphrases of varying lengths. We overcome these modeling shortcomings by addressing keyphrase extraction as a sequential labeling task in this paper. We explore a basic set of features commonly used in NLP tasks as well as predictions from various unsupervised methods to train our taggers. In addition to a more natural modeling for the keyphrase extraction problem, we show that tagging models yield significant performance benefits over existing state-of-the-art extraction methods.

Yong Liu, Peilin Zhao, Xin Liu et al.

Social recommender systems exploit users' social relationships to improve the recommendation accuracy. Intuitively, a user tends to trust different subsets of her social friends, regarding with different scenarios. Therefore, the main challenge of social recommendation is to exploit the optimal social dependency between users for a specific recommendation task. In this paper, we propose a novel recommendation method, named probabilistic relational matrix factorization (PRMF), which aims to learn the optimal social dependency between users to improve the recommendation accuracy, with or without users' social relationships. Specifically, in PRMF, the latent features of users are assumed to follow a matrix variate normal (MVN) distribution. The positive and negative dependency between users are modeled by the row precision matrix of the MVN distribution. Moreover, we have also proposed an efficient alternating algorithm to solve the optimization problem of PRMF. The experimental results on real datasets demonstrate that the proposed PRMF method outperforms state-of-the-art social recommendation approaches, in terms of root mean square error (RMSE) and mean absolute error (MAE).

Jian-Ping Mei, Chee-Keong Kwoh, Peng Yang et al.

Classification is one of the most popular and widely used supervised learning tasks, which categorizes objects into predefined classes based on known knowledge. Classification has been an important research topic in machine learning and data mining. Different classification methods have been proposed and applied to deal with various real-world problems. Unlike unsupervised learning such as clustering, a classifier is typically trained with labeled data before being used to make prediction, and usually achieves higher accuracy than unsupervised one. In this paper, we first define classification and then review several representative methods. After that, we study in details the application of classification to a critical problem in drug discovery, i.e., drug-target prediction, due to the challenges in predicting possible interactions between drugs and targets.

Peng Yang, Xiaoquan Su, Le Ou-Yang et al.

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural patterns. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.