arXiv subjects

Gang Fu

Publications and source records attributed to Gang Fu.

23 records · Page 2Linked to original sources

arXiv2019

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.

cs.IR↗

arXiv2017

Deep & Cross Network for Ad Click Predictions

Feature engineering has been the key to the success of many prediction models. However, the process is non-trivial and often requires manual feature engineering or exhaustive searching. DNNs are able to automatically learn feature interactions; however, they generate all the interactions implicitly, and are not necessarily efficient in learning all types of cross features. In this paper, we propose the Deep & Cross Network (DCN) which keeps the benefits of a DNN model, and beyond that, it introduces a novel cross network that is more efficient in learning certain bounded-degree feature interactions. In particular, DCN explicitly applies feature crossing at each layer, requires no manual feature engineering, and adds negligible extra complexity to the DNN model. Our experimental results have demonstrated its superiority over the state-of-art algorithms on the CTR prediction dataset and dense classification dataset, in terms of both model accuracy and memory usage.

cs.LG↗

arXiv2016

Greedy Column Subset Selection: New Bounds and Distributed Algorithms

The problem of column subset selection has recently attracted a large body of research, with feature selection serving as one obvious and important application. Among the techniques that have been applied to solve this problem, the greedy algorithm has been shown to be quite effective in practice. However, theoretical guarantees on its performance have not been explored thoroughly, especially in a distributed setting. In this paper, we study the greedy algorithm for the column subset selection problem from a theoretical and empirical perspective and show its effectiveness in a distributed setting. In particular, we provide an improved approximation guarantee for the greedy algorithm which we show is tight up to a constant factor, and present the first distributed implementation with provable approximation factors. We use the idea of randomized composable core-sets, developed recently in the context of submodular maximization. Finally, we validate the effectiveness of this distributed algorithm via an empirical study.

cs.DS↗

arXiv2015

On Reasoning with RDF Statements about Statements using Singleton Property Triples

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties.

cs.AI↗

arXiv2015

Exposing Provenance Metadata Using Different RDF Models

A standard model for exposing structured provenance metadata of scientific assertions on the Semantic Web would increase interoperability, discoverability, reliability, as well as reproducibility for scientific discourse and evidence-based knowledge discovery. Several Resource Description Framework (RDF) models have been proposed to track provenance. However, provenance metadata may not only be verbose, but also significantly redundant. Therefore, an appropriate RDF provenance model should be efficient for publishing, querying, and reasoning over Linked Data. In the present work, we have collected millions of pairwise relations between chemicals, genes, and diseases from multiple data sources, and demonstrated the extent of redundancy of provenance information in the life science domain. We also evaluated the suitability of several RDF provenance models for this crowdsourced data set, including the N-ary model, the Singleton Property model, and the Nanopublication model. We examined query performance against three commonly used large RDF stores, including Virtuoso, Stardog, and Blazegraph. Our experiments demonstrate that query performance depends on both RDF store as well as the RDF provenance model.

cs.DB↗