edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

Deep Multi-view Learning to Rank

We study the problem of learning to rank from multiple information sources. Though multi-view learning and learning to rank have been studied extensively leading to a wide range of applications, multi-view learning to rank as a synergy of both topics has received little attention. The aim of the paper is to propose a composite ranking method while keeping a close correlation with the individual rankings simultaneously. We present a generic framework for multi-view subspace learning to rank (MvSL2R), and two novel solutions are introduced under the framework. The first solution captures information of feature mappings from within each view as well as across views using autoencoder-like networks. Novel feature embedding methods are formulated in the optimization of multi-view unsupervised and discriminant autoencoders. Moreover, we introduce an end-to-end solution to learning towards both the joint ranking objective and the individual rankings. The proposed solution enhances the joint ranking with minimum view-specific ranking loss, so that it can achieve the maximum global view agreements in a single optimization process. The proposed method is evaluated on three different ranking problems, i.e. university ranking, multi-view lingual text ranking and image data ranking, providing superior results compared to related methods.Comment: Published at IEEE TKD

Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Geo-Spotting: Mining Online Location-based Services for Optimal Retail Store Placement

The problem of identifying the optimal location for a new retail store has been the focus of past research, especially in the field of land economy, due to its importance in the success of a business. Traditional approaches to the problem have factored in demographics, revenue and aggregated human flow statistics from nearby or remote areas. However, the acquisition of relevant data is usually expensive. With the growth of location-based social networks, fine grained data describing user mobility and popularity of places has recently become attainable. In this paper we study the predictive power of various machine learning features on the popularity of retail stores in the city through the use of a dataset collected from Foursquare in New York. The features we mine are based on two general signals: geographic, where features are formulated according to the types and density of nearby places, and user mobility, which includes transitions between venues or the incoming flow of mobile users from distant areas. Our evaluation suggests that the best performing features are common across the three different commercial chains considered in the analysis, although variations may exist too, as explained by heterogeneities in the way retail facilities attract users. We also show that performance improves significantly when combining multiple features in supervised learning algorithms, suggesting that the retail success of a business may depend on multiple factors.Comment: Proceedings of the 19th ACM SIGKDD international conference on Knowledge discovery and data mining, Chicago, 2013, Pages 793-80

Prediction of microbial communities for urban metagenomics using neural network approach.

BACKGROUND:Microbes are greatly associated with human health and disease, especially in densely populated cities. It is essential to understand the microbial ecosystem in an urban environment for cities to monitor the transmission of infectious diseases and detect potentially urgent threats. To achieve this goal, the DNA sample collection and analysis have been conducted at subway stations in major cities. However, city-scale sampling with the fine-grained geo-spatial resolution is expensive and laborious. In this paper, we introduce MetaMLAnn, a neural network based approach to infer microbial communities at unsampled locations given information reflecting different factors, including subway line networks, sampling material types, and microbial composition patterns. RESULTS:We evaluate the effectiveness of MetaMLAnn based on the public metagenomics dataset collected from multiple locations in the New York and Boston subway systems. The experimental results suggest that MetaMLAnn consistently performs better than other five conventional classifiers under different taxonomic ranks. At genus level, MetaMLAnn can achieve F1 scores of 0.63 and 0.72 on the New York and the Boston datasets, respectively. CONCLUSIONS:By exploiting heterogeneous features, MetaMLAnn captures the hidden interactions between microbial compositions and the urban environment, which enables precise predictions of microbial communities at unmeasured locations