Graph embedding on biomedical networks: methods, applications and evaluations

To Embed or Not: Network Embedding as a Paradigm in Computational Biology

(2019) Walter Nelson et al.   Frontiers in Genetics

deepNF: deep network fusion for protein function prediction

(2018) Vladimir Gligorijević et al.   BIOINFORMATICS

Modeling polypharmacy side effects with graph convolutional networks

(2018) Marinka Zitnik et al.   BIOINFORMATICS

Predicting drug-disease associations by using similarity constrained matrix factorization

(2018) Wen Zhang et al.   BMC BIOINFORMATICS

Deep learning improves prediction of drug–drug and drug–food interactions

(2018) Jae Yong Ryu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Comparative Toxicogenomics Database: update 2019

(2018) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Manifold regularized matrix factorization for drug-drug interaction prediction

(2018) Wen Zhang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

(2018) Wen Zhang et al.   PLoS Computational Biology

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records

(2018) Casey N. Ta et al.   Scientific Data

Drug-target interaction prediction using ensemble learning and dimensionality reduction

(2017) Ali Ezzat et al.   METHODS

Predicting protein–protein interactions from protein sequences by a stacked sparse autoencoder deep neural network

(2017) Yan-Bin Wang et al.   Molecular BioSystems

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

An improved sequence-based prediction protocol for protein-protein interactions using amino acids substitution matrix and rotation forest ensemble classifiers

(2017) Zhu-Hong You et al.   NEUROCOMPUTING

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Learning a Health Knowledge Graph from Electronic Medical Records

(2017) Maya Rotmensch et al.   Scientific Reports

Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

(2016) Hoo-Chang Shin et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

Matrix Factorization-Based Prediction of Novel Drug Indications by Integrating Genomic Space

(2015) Wen Dai et al.   Computational and Mathematical Methods in Medicine

Data Fusion by Matrix Factorization

(2015) Marinka Zitnik et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Building the graph of medicine from millions of clinical narratives

(2014) Samuel G. Finlayson et al.   Scientific Data

Increasing the reliability of protein–protein interaction networks via non-convex semantic embedding

(2013) Lin Zhu et al.   NEUROCOMPUTING

Fast prediction of protein–protein interaction sites based on Extreme Learning Machines

(2013) Debby D. Wang et al.   NEUROCOMPUTING

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

Link prediction in complex networks: A survey

(2010) Linyuan Lü et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS