cran: node2vec | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02264-8

GeneWalk identifies relevant gene functions for a biological context using network representation learning
Cited by: 26
Author(s): Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, L. Stirling Churchman
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12918-018-0662-y

Integrating node embeddings and biological annotations for genes to predict disease-gene associations
Cited by: 27
Author(s): Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu, Xiaoli Li
Software Mentions: 11
Published: almost 6 years ago

10.1186/s12859-021-04055-1

Juxtapose: a gene-embedding approach for comparing co-expression networks
Cited by: 8
Author(s): Katie Ovens, Farhad Maleki, B. Frank Eames, Ian McQuillan
Software Mentions: 10
Published: over 3 years ago

10.1186/s13062-018-0214-9

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach
Cited by: 13
Author(s): Léon-Charles Tranchevent, Petr V. Nazarov, Tony Kaoma, Georges Pierre Schmartz, Arnaud Muller, Sang Yoon Kim, Jagath C. Rajapakse, Francisco Azuaje
Software Mentions: 10
Published: almost 7 years ago

10.7717/peerj-cs.521

LinkPred: a high performance library for link prediction in complex networks
Cited by: 0
Author(s): Said Kerrache
Software Mentions: 8
Published: over 3 years ago

10.1155/2021/5573740

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning
Cited by: 10
Author(s): Simon Wein, Gustavo Deco, Ana Maria Tomé, Markus Goldhacker, Wilhelm M. Malloni, Mark W. Greenlee, Elmar Lang
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1009382

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Cited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: about 3 years ago

10.1186/s13321-019-0342-y

KMR: knowledge-oriented medicine representation learning for drug–drug interaction and similarity computation
Cited by: 16
Author(s): Ying Shen, Kun Yuan, Min Yang, Buzhou Tang, Yaliang Li, Nan Du, Kai Lei
Software Mentions: 7
Published: over 5 years ago

10.1007/s10994-020-05890-8

Propositionalization and embeddings: two sides of the same coin
Cited by: 20
Author(s): Nada Lavrač, Blaž Škrlj, Marko Robnik–Šikonja
Software Mentions: 6
Published: over 4 years ago

10.1186/s13321-020-00447-2

DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques
Cited by: 54
Author(s): Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori, Magbubah Essack
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-020-03816-8

Graph embeddings on gene ontology annotations for protein–protein interaction prediction
Cited by: 14
Author(s): Xiaoshi Zhong, Jagath C. Rajapakse
Software Mentions: 6
Published: almost 4 years ago

10.1128/mSystems.01296-20

Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli
Cited by: 16
Author(s): Natan Nagar, Noa Ecker, Gil Loewenthal, Oren Avram, Daniella Ben-Meir, Dvora Biran, Eliora Z. Ron, Tal Pupko
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13321-021-00552-w

DTi2Vec: Drug–target interaction prediction using network embedding and ensemble learning
Cited by: 20
Author(s): Maha A. Thafar, Rawan S. Olayan, Somayah Albaradei, Vladimir B. Bajic, Takashi Gojobori, Magbubah Essack, Xin Gao
Software Mentions: 6
Published: about 3 years ago

10.1016/j.csbj.2020.05.017

Constructing knowledge graphs and their biomedical applications
Cited by: 115
Author(s): David N. Nicholson, Casey S. Greene
Software Mentions: 6
Published: almost 5 years ago

10.3389/fdata.2021.699070

Unified Representation of Twitter and Online News Using Graph and Entities
Cited by: 1
Author(s): Munira Syed, Daheng Wang, Meng Jiang, Oliver Conway, Vishal Juneja, Sriram Subramanian, Nitesh V. Chawla
Software Mentions: 6
Published: about 3 years ago

10.1007/s10994-020-05882-8

Embedding-based Silhouette community detection
Cited by: 10
Author(s): Blaž Škrlj, Jan Kralj, Nada Lavrač
Software Mentions: 6
Published: over 4 years ago

10.3389/fnins.2021.605115

Diagnosis of Alzheimer’s Disease Using Brain Network
Cited by: 12
Author(s): Ramesh Kumar Lama, Goo‐Rak Kwon
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcell.2021.732370

An Integrative Network Science and Artificial Intelligence Drug Repurposing Approach for Muscle Atrophy in Spaceflight Microgravity
Cited by: 2
Author(s): Vidya Manian, Jairo Orozco-Sandoval, Victor Díaz-Martínez
Software Mentions: 5
Published: about 3 years ago

10.3389/frma.2021.644614

PubMed-Scale Chemical Concept Embeddings Reconstruct Physical Protein Interaction Networks
Cited by: 0
Author(s): Blaž Škrlj, Enja Kokalj, Nada Lavrač
Software Mentions: 5
Published: over 3 years ago

10.3389/fncom.2018.00095

Brain Network Analysis and Classification Based on Convolutional Neural Network
Cited by: 18
Author(s): Meng Liu, Jing Xiang
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pcbi.1008229

DeepHE: Accurately predicting human essential genes based on deep learning
Cited by: 24
Author(s): Xue Zhang, Wangxin Xiao, Weijia Xiao
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0248552

KG2Vec: A node2vec-based vectorization model for knowledge graph
Cited by: 11
Author(s): YueQun Wang, Liyan Dong, XiaoQuan Jiang, Xintao Ma, Yongli Li, Hao Zhang
Software Mentions: 5
Published: over 3 years ago

10.3389/fncom.2020.603765

WGEVIA: A Graph Level Embedding Method for Microcircuit Data
Cited by: 1
Author(s): Xiaomin Wu, Shuvra S. Bhattacharyya, Rong Chen
Software Mentions: 5
Published: almost 4 years ago

10.1007/s41109-020-00257-3

Evolving network representation learning based on random walks
Cited by: 8
Author(s): Farzaneh Heidari, Manos Papagelis
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0218264

Predicting biomedical relationships using the knowledge and graph embedding cascade model
Cited by: 18
Author(s): Xiaomin Liang, Daifeng Li, Min Song, Andrew D. Madden, Ying Ding, Yi Bu
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-017-12586-y

The Hidden Flow Structure and Metric Space of Network Embedding Algorithms Based on Random Walks
Cited by: 11
Author(s): Weiwei Gu, L. Gong, Xiaodan Lou, Jiang Zhang
Software Mentions: 5
Published: about 7 years ago

10.1186/s13321-021-00513-3

Deep learning integration of molecular and interactome data for protein–compound interaction prediction
Cited by: 4
Author(s): Narumi Watanabe, Yuuto Ohnuki, Yasubumi Sakakibara
Software Mentions: 4
Published: over 3 years ago

10.3389/fdata.2019.00002

Deep Representation Learning for Social Network Analysis
Cited by: 39
Author(s): Qiaoyu Tan, Ninghao Liu, Xia Hu
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.626500

Identification of Protein Subcellular Localization With Network and Functional Embeddings
Cited by: 38
Author(s): Xiaoyong Pan, Hao Li, Tao Zeng, Zhandong Li, Lei Chen, Tao Huang, Yi Cai
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-019-3284-5

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings
Cited by: 56
Author(s): Remzi Çelebi, H. Turgut Uyar, Erkan Yasar, Özgür Gümüş, Oğuz Dikenelli, Michel Dumontier
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms22189983

Comprehensive Survey of Recent Drug Discovery Using Deep Learning
Cited by: 43
Author(s): Kim Jintae, Sera Park, Dongbo Min, Wankyu Kim
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2021.738274

iCDI-W2vCom: Identifying the Ion Channel–Drug Interaction in Cellular Networking Based on word2vec and node2vec
Cited by: 4
Author(s): Jie Zheng, Xuan Xiao, Wang-Ren Qiu
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-021-85255-w

Leveraging graph-based hierarchical medical entity embedding for healthcare applications
Cited by: 7
Author(s): Tong Wu, Yunlong Wang, Yue Wang, Emily Zhao, Yilian Yuan
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-79422-8

FlavorGraph: a large-scale food-chemical graph for generating food representations and recommending food pairings
Cited by: 13
Author(s): Donghyeon Park, Keonwoo Kim, Seoyoon Kim, Michael Spranger, Jaewoo Kang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-6272-2

GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings
Cited by: 15
Author(s): Xiaoshi Zhong, Rama Kaalia, Jagath C. Rajapakse
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-019-3076-y

DeepEP: a deep learning framework for identifying essential proteins
Cited by: 36
Author(s): Min Zeng, Min Li, Fang‐Xiang Wu, Yaohang Li, Yi Pan
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12920-019-0605-5

Prediction of comorbid diseases using weighted geometric embedding of human interactome
Cited by: 8
Author(s): Pakeeza Akram, Li Liao
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12918-019-0694-y

GNE: a deep learning framework for gene network inference by aggregating biological information
Cited by: 29
Author(s): Kishan Kc, Rui Li, Feng Cui, Qi Yu, Anne R. Haake
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/6248686

PmDNE: Prediction of miRNA-Disease Association Based on Network Embedding and Network Similarity Analysis
Cited by: 2
Author(s): Junyi Li, Ying Liu, Zhongqing Zhang, Bo Liu, Yadong Wang
Software Mentions: 4
Published: almost 4 years ago

10.1093/bib/bbaa257

Biological network analysis with deep learning
Cited by: 88
Author(s): Giulia Muzio, Leslie O’Bray, Karsten Borgwardt
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-021-04327-w

DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding
Cited by: 14
Author(s): Yue Yang, Shan He
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj-cs.357

Survey on graph embeddings and their applications to machine learning problems on graphs
Cited by: 48
Author(s): Ilya Makarov, Dmitrii Kiselev, Nikita Nikitinsky, Lovro Šubelj
Software Mentions: 4
Published: almost 4 years ago

10.1101/2020.08.17.254839

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response
Cited by: 5
Author(s): Justin Reese, Deepak Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica Munoz‐Torres, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0221172

SimNet: Similarity-based network embeddings with mean commute time
Cited by: 9
Author(s): M. Amin Khajehnejad
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0224684

User abnormal behavior recommendation via multilayer network
Cited by: 6
Author(s): Chengyun Song, Weiyi Liu, Zhining Liu, Xiaoyang Liu
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0244430

PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks
Cited by: 7
Author(s): Seyyede Fatemeh Seyyedsalehi, Mahdieh Soleymani, Hamid R. Rabiee, Mohammad R. K. Mofrad
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-019-2914-2

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Cited by: 33
Author(s): Zheng Gao, Gang Fu, Cheng Ouyang, Satoshi Tsutsui, Xiaozhong Liu, Jeremy J. Yang, Christopher R Gessner, Brian Foote, David Wild, Ying Ding, Qi Yu
Software Mentions: 4
Published: over 5 years ago

10.1016/j.csbj.2019.02.002

Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network
Cited by: 18
Author(s): Ning Wang, Peng Li, Xiaochen Hu, Kuo Yang, Yonghong Peng, Qiang Zhu, Runshun Zhang, Zhuye Gao, Hao Xu, Baoyan Liu, Jianxin Chen, Xuezhong Zhou
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0242723

A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins
Cited by: 1
Author(s): Stavros Makrodimitris, Marcel J. T. Reinders, Roeland van Ham
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-021-03971-6

Data-driven biological network alignment that uses topological, sequence, and functional information
Cited by: 2
Author(s): Shawn Gu, Tijana Milenković
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-019-3063-3

A network embedding-based multiple information integration method for the MiRNA-disease association prediction
Cited by: 50
Author(s): Yuchong Gong, Yanqing Niu, Wen Zhang, LI Xiao-hong
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-07223-4

gCAnno: a graph-based single cell type annotation method
Cited by: 0
Author(s): Xiaofei Yang, Shenghan Gao, Ting-Jie Wang, Boyu Yang, Ningxin Dang, Kai Ye
Software Mentions: 3
Published: about 4 years ago

10.1186/s12911-018-0592-z

Heterogeneous network propagation for herb target identification
Cited by: 6
Author(s): Kuo Yang, Guangming Liu, Ning Wang, Runshun Zhang, Jian Yu, Jianxin Chen, Xuezhong Zhou
Software Mentions: 3
Published: over 6 years ago

10.1016/j.patter.2020.100155

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response
Cited by: 54
Author(s): Justin Reese, Deepak Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica Munoz‐Torres, Melissa Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall
Software Mentions: 3
Published: almost 4 years ago

10.3390/pharmaceutics11080377

Comparison of Target Features for Predicting Drug-Target Interactions by Deep Neural Network Based on Large-Scale Drug-Induced Transcriptome Data
Cited by: 22
Author(s): Hanbi Lee, Wankyu Kim
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0238915

Graph embedding-based novel protein interaction prediction via higher-order graph convolutional network
Cited by: 25
Author(s): Zewen Xiao, Yue Deng
Software Mentions: 3
Published: about 4 years ago

10.3390/cells8090977

A Novel Computational Model for Predicting microRNA–Disease Associations Based on Heterogeneous Graph Convolutional Networks
Cited by: 53
Author(s): Chunyan Li, Hongju Liu, Qian Hu, Jinlong Que, Junfeng Yao
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.700061

DeepGP: An Integrated Deep Learning Method for Endocrine Disease Gene Prediction Using Omics Data
Cited by: 1
Author(s): Ningyi Zhang, Haoyan Wang, Xu Chen, Liyuan Zhang, Tianyi Zang
Software Mentions: 3
Published: over 3 years ago

10.3389/fchem.2019.00782

Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities
Cited by: 82
Author(s): Maha A. Thafar, Arwa Bin Raies, Somayah Albaradei, Magbubah Essack, Vladimir B. Bajic
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2021.728333

Discovering Cerebral Ischemic Stroke Associated Genes Based on Network Representation Learning
Cited by: 4
Author(s): Haijie Liu, Liping Hou, Shanhu Xu, He Li, Xiuju Chen, Juan Gao, Ziwen Wang, Bo Han, Xiaoli Liu, Shu Wan
Software Mentions: 3
Published: about 3 years ago

10.1016/j.gpb.2020.11.003

Computational Screening of Phase-separating Proteins
Cited by: 27
Author(s): Boyan Shen, Zhaoming Chen, Chunyu Yu, Taoyu Chen, Minglei Shi, Tingting Li
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-020-77766-9

SkipGNN: predicting molecular interactions with skip-graph networks
Cited by: 43
Author(s): Kexin Huang, Cao Xiao, Lucas M. Glass, Marinka Žitnik, Jimeng Sun
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-87987-1

MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach
Cited by: 14
Author(s): Léo Pio-Lopez, Alberto Valdeolivas, Laurent Tichit, Élisabeth Rémy, Anaı̈s Baudot
Software Mentions: 3
Published: over 3 years ago

10.3390/s21092911

Vision–Language–Knowledge Co-Embedding for Visual Commonsense Reasoning
Cited by: 3
Author(s): JaeYun Lee, In-Cheol Kim
Software Mentions: 3
Published: over 3 years ago

10.2196/18417

Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models
Cited by: 19
Author(s): Bharath Dandala, Venkata Joopudi, Ching-Huei Tsou, Jennifer J. Liang, Parthasarathy Suryanarayanan
Software Mentions: 3
Published: over 4 years ago

10.3390/jpm11040300

Knowledge Graphs for COVID-19: An Exploratory Review of the Current Landscape
Cited by: 16
Author(s): A. Chatterjee, Cosimo Nardi, Cary Oberije, Philippe Lambin
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2018.00248

Prediction of Drug–Gene Interaction by Using Metapath2vec
Cited by: 28
Author(s): Siyi Zhu, Jiaxin Bing, Xiaoping Min, Chen Lin, Xiangxiang Zeng
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00381

To Embed or Not: Network Embedding as a Paradigm in Computational Biology
Cited by: 123
Author(s): William H. Nelson, Marinka Žitnik, Bo Wang, Jure Leskovec, Anna Goldenberg, Roded Sharan
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.650821

GADTI: Graph Autoencoder Approach for DTI Prediction From Heterogeneous Network
Cited by: 10
Author(s): Zhixian Liu, Yi‐Ping Phoebe Chen, Wei Lan, Haiming Pan, Xinkun Hao, Shirui Pan
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00328

Predicting the Disease Genes of Multiple Sclerosis Based on Network Representation Learning
Cited by: 7
Author(s): Haijie Liu, Jiaojiao Guan, He Li, Zhijie Bao, Qingmei Wang, Xun Luo, Hansheng Xue
Software Mentions: 2
Published: over 4 years ago

10.3389/fnbot.2021.665055

SeBioGraph: Semi-supervised Deep Learning for the Graph via Sustainable Knowledge Transfer
Cited by: 3
Author(s): Yugang Ma, Qing Li, Nan Hu, Lili Li
Software Mentions: 2
Published: over 3 years ago

10.3389/fnins.2019.01387

Multi-Task Learning Based Network Embedding
Cited by: 9
Author(s): Shanfeng Wang, Qixiang Wang, Maoguo Gong
Software Mentions: 2
Published: almost 5 years ago

10.3390/e23040403

Multi-Scale Aggregation Graph Neural Networks Based on Feature Similarity for Semi-Supervised Learning
Cited by: 4
Author(s): Xun Zhang, Lanyan Yang, Bin Zhang, Ying Liu, Dong Jiang, Xiaohai Qin, Ming Hao
Software Mentions: 2
Published: over 3 years ago

10.3389/fnins.2020.00001

Multi-Task Network Representation Learning
Cited by: 9
Author(s): Yu Xie, Peixuan Jin, Maoguo Gong, Chen Zhang, Bin Yu
Software Mentions: 2
Published: almost 5 years ago

10.3390/e22020197

Optimizing Variational Graph Autoencoder for Community Detection with Dual Optimization
Cited by: 13
Author(s): Jun Jin Choong, Xin Liu, Tsuyoshi Murata
Software Mentions: 2
Published: almost 5 years ago

10.3390/genes11060668

A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis
Cited by: 14
Author(s): Daniel Bean, Ammar Al‐Chalabi, Richard Dobson, Alfredo Iacoangeli
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0188577

Analyzing cross-college course enrollments via contextual graph mining
Cited by: 4
Author(s): Yongzhen Wang, Xiaozhong Liu, Yan Chen
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-021-04300-7

An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information
Cited by: 2
Author(s): Shiyuan Li, Zhen Zhang, Xueyong Li, Tan Yang, Lei Wang
Software Mentions: 2
Published: about 3 years ago

10.1007/s10796-021-10131-x

The Role of Artificial Intelligence in Fighting the COVID-19 Pandemic
Cited by: 56
Author(s): Francesco Piccialli, Vincenzo Schiano di Cola, Fabio Giampaolo, Salvatore Cuomo
Software Mentions: 2
Published: over 3 years ago

10.1186/s13326-018-0188-7

EAPB: entropy-aware path-based metric for ontology quality
Cited by: 1
Author(s): Ying Shen, Daoyuan Chen, Buzhou Tang, Min Yang, Kai Lei
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1008186

A new Graph Gaussian embedding method for analyzing the effects of cognitive training
Cited by: 17
Author(s): Mengjia Xu, Zhijiang Wang, Haifeng Zhang, Dimitrios Pantazis, Huali Wang, Quanzheng Li
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1008998

PRER: A patient representation with pairwise relative expression of proteins on biological networks
Cited by: 0
Author(s): Halil İbrahim Kuru, Mustafa Büyüközkan, Öznur Taştan
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj-cs.172

Dual network embedding for representing research interests in the link prediction problem on co-authorship networks
Cited by: 23
Author(s): Ilya Makarov, Olga Gerasimova, Pavel Sulimov, Leonid Zhukov
Software Mentions: 2
Published: almost 6 years ago

10.1093/bioinformatics/btaa150

Supervised learning is an accurate method for network-based gene classification
Cited by: 23
Author(s): Renming Liu, Christopher Mancuso, Anna Yannakopoulos, Kayla A Johnson, Arjun Krishnan
Software Mentions: 2
Published: over 4 years ago

10.1073/pnas.1911030117

The impossibility of low-rank representations for triangle-rich complex networks
Cited by: 33
Author(s): C. Seshadhri, Aneesh Sharma, Andrew Stolman, Ashish Goel
Software Mentions: 2
Published: over 4 years ago

10.1186/s12911-019-0880-2

Detection of medical text semantic similarity based on convolutional neural network
Cited by: 19
Author(s): Tao Zheng, Yimei Gao, Fei Wang, Chenchen Fan, Xingzhi Fu, Mei Li, Ya Zhang, Shaodian Zhang, Handong Ma
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-69379-z

Identifying critical nodes in temporal networks by network embedding
Cited by: 11
Author(s): Enyu Yu, Yan Fu, Xiao Chen, Mei Xie, Duanbing Chen
Software Mentions: 2
Published: over 4 years ago

10.2196/29570

Social Media Polarization and Echo Chambers in the Context of COVID-19: Case Study
Cited by: 25
Author(s): Julie Jiang, Xiang Ren, Emilio Ferrara
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-3056-2

Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach
Cited by: 10
Author(s): Mohan Timilsina, Haixuan Yang, Ratnesh Sahay, Dietrich Rebholz‐Schuhmann
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-018-2200-8

Relation extraction for biological pathway construction using node2vec
Cited by: 14
Author(s): Munui Kim, Seung Han Baek, Min Song
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-85826-x

Discovering latent node Information by graph attention network
Cited by: 5
Author(s): Weiwei Gu, Fei Gao, Xiaodan Lou, Jiang Zhang
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms20236046

DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model
Cited by: 5
Author(s): Jiacheng Wang, Jingpu Zhang, Yideng Cai, Lei Deng
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-92427-1

An information theoretic approach to link prediction in multiplex networks
Cited by: 4
Author(s): Seyed Hossein Jafari, Amir Mahdi Abdolhosseini-Qomi, Masoud Asadpour, Maseud Rahgozar, Naser Yazdani
Software Mentions: 2
Published: over 3 years ago

10.3390/s19245518

A Spatial Adaptive Algorithm Framework for Building Pattern Recognition Using Graph Convolutional Networks
Cited by: 14
Author(s): Weijia Bei, Mingqiang Guo, Ying Huang
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22073378

Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia
Cited by: 3
Author(s): Alfonso Martín-Bernabé, Josep Tarragó‐Celada, Valérie Cunin, Sylvie Michelland, Roberto Cortés, Johann Poignant, Cyril Boyault, Walid Rachidi, Sandrine Bourgoin-Voillard, Marta Cascante, Michel Sève
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2364-2

Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks
Cited by: 6
Author(s): Xiaoxia Liu, Zhihao Yang, Shengtian Sang, Ziwei Zhou, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Bo Xu
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2021.657182

MGRL: Predicting Drug-Disease Associations Based on Multi-Graph Representation Learning
Cited by: 7
Author(s): Bo-Wei Zhao, Zhu‐Hong You, Leon Wong, Ping Zhang, Haoyuan Li, Lei Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2019.00003

Predicting Gene Ontology Function of Human MicroRNAs by Integrating Multiple Networks
Cited by: 36
Author(s): Lei Deng, Jiacheng Wang, Jingpu Zhang
Software Mentions: 2
Published: almost 6 years ago

10.3389/fbioe.2020.00418

Disease Module Identification Based on Representation Learning of Complex Networks Integrated From GWAS, eQTL Summaries, and Human Interactome
Cited by: 21
Author(s): Tao Wang, Qidi Peng, Bo Liu, Yongzhuang Liu, Yadong Wang
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.00807

Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes
Cited by: 3
Author(s): Kunjie Fan, Yan Zhang
Software Mentions: 2
Published: over 4 years ago

Projects: cran: node2vec

Papers Mentioning node2vec 104