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For: Kong Y, Yu T. A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data. Bioinformatics 2018;34:3727-3737. [PMID: 29850911 PMCID: PMC6198851 DOI: 10.1093/bioinformatics/bty429] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/30/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Zeng Y, Zhang Y, Xiao Z, Sui H. A multi-classification deep neural network for cancer type identification from high-dimension, small-sample and imbalanced gene microarray data. Sci Rep 2025;15:5239. [PMID: 39939378 PMCID: PMC11822135 DOI: 10.1038/s41598-025-89475-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 02/05/2025] [Indexed: 02/14/2025]  Open
2
Li R, Yi H, Ma S. A Selective Review of Network Analysis Methods for Gene Expression Data. Methods Mol Biol 2025;2880:293-307. [PMID: 39900765 DOI: 10.1007/978-1-0716-4276-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2025]
3
Khullar S, Huang X, Ramesh R, Svaren J, Wang D. NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation. BIOINFORMATICS ADVANCES 2024;5:vbae206. [PMID: 40260118 PMCID: PMC12011367 DOI: 10.1093/bioadv/vbae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 10/22/2024] [Accepted: 12/18/2024] [Indexed: 04/23/2025]
4
Sun C, Liu ZP. Discovering explainable biomarkers for breast cancer anti-PD1 response via network Shapley value analysis. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024;257:108481. [PMID: 39488042 DOI: 10.1016/j.cmpb.2024.108481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 10/20/2024] [Accepted: 10/24/2024] [Indexed: 11/04/2024]
5
Liang H, Luo H, Sang Z, Jia M, Jiang X, Wang Z, Cong S, Yao X. GREMI: An Explainable Multi-Omics Integration Framework for Enhanced Disease Prediction and Module Identification. IEEE J Biomed Health Inform 2024;28:6983-6996. [PMID: 39110558 DOI: 10.1109/jbhi.2024.3439713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
6
Jagadesh P, Khan AH, Priya BS, Asheeka A, Zoubir Z, Magbool HM, Alam S, Bakather OY. Artificial neural network, machine learning modelling of compressive strength of recycled coarse aggregate based self-compacting concrete. PLoS One 2024;19:e0303101. [PMID: 38739642 PMCID: PMC11090367 DOI: 10.1371/journal.pone.0303101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]  Open
7
Chereda H, Leha A, Beißbarth T. Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. Artif Intell Med 2024;151:102840. [PMID: 38658129 DOI: 10.1016/j.artmed.2024.102840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 04/26/2024]
8
Nissar I, Alam S, Masood S, Kashif M. MOB-CBAM: A dual-channel attention-based deep learning generalizable model for breast cancer molecular subtypes prediction using mammograms. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024;248:108121. [PMID: 38531147 DOI: 10.1016/j.cmpb.2024.108121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
9
Yang B, Wang L, Bao W. Identify Diabetes-related Targets based on ForgeNet_GPC. Curr Comput Aided Drug Des 2024;20:1042-1054. [PMID: 38173214 DOI: 10.2174/0115734099258183230929173855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
10
Tian L, Yu T. An integrated deep learning framework for the interpretation of untargeted metabolomics data. Brief Bioinform 2023;24:bbad244. [PMID: 37369636 DOI: 10.1093/bib/bbad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]  Open
11
Tian L, Wu W, Yu T. Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features. Biomolecules 2023;13:1153. [PMID: 37509188 PMCID: PMC10377046 DOI: 10.3390/biom13071153] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]  Open
12
Lee S, Jung H, Park J, Ahn J. Accurate Prediction of Cancer Prognosis by Exploiting Patient-Specific Cancer Driver Genes. Int J Mol Sci 2023;24:ijms24076445. [PMID: 37047418 PMCID: PMC10095073 DOI: 10.3390/ijms24076445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]  Open
13
Alharbi F, Vakanski A. Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review. Bioengineering (Basel) 2023;10:bioengineering10020173. [PMID: 36829667 PMCID: PMC9952758 DOI: 10.3390/bioengineering10020173] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]  Open
14
Hou X, Hou J, Huang G. Bi-dimensional principal gene feature selection from big gene expression data. PLoS One 2022;17:e0278583. [PMID: 36477666 PMCID: PMC9728919 DOI: 10.1371/journal.pone.0278583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022]  Open
15
Wang C, Lye X, Kaalia R, Kumar P, Rajapakse JC. Deep learning and multi-omics approach to predict drug responses in cancer. BMC Bioinformatics 2022;22:632. [PMID: 36443676 PMCID: PMC9703655 DOI: 10.1186/s12859-022-04964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 11/29/2022]  Open
16
Sparse multi-label feature selection via dynamic graph manifold regularization. INT J MACH LEARN CYB 2022. [DOI: 10.1007/s13042-022-01679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
17
Guo X, Han J, Song Y, Yin Z, Liu S, Shang X. Using expression quantitative trait loci data and graph-embedded neural networks to uncover genotype–phenotype interactions. Front Genet 2022;13:921775. [PMID: 36046233 PMCID: PMC9421127 DOI: 10.3389/fgene.2022.921775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022]  Open
18
Yang B, Bao W, Hong S. Alzheimer-Compound Identification Based on Data Fusion and forgeNet_SVM. Front Aging Neurosci 2022;14:931729. [PMID: 35959292 PMCID: PMC9357977 DOI: 10.3389/fnagi.2022.931729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]  Open
19
Kumar R, Khatri A, Acharya V. Deep learning uncovers distinct behavior of rice network to pathogens response. iScience 2022;25:104546. [PMID: 35754717 PMCID: PMC9218438 DOI: 10.1016/j.isci.2022.104546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/06/2022] [Accepted: 06/02/2022] [Indexed: 12/15/2022]  Open
20
Rezaee K, Jeon G, Khosravi MR, Attar HH, Sabzevari A. Deep learning‐based microarray cancer classification and ensemble gene selection approach. IET Syst Biol 2022;16:120-131. [PMID: 35790076 PMCID: PMC9290776 DOI: 10.1049/syb2.12044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 05/31/2022] [Indexed: 12/19/2022]  Open
21
EGFAFS: A Novel Feature Selection Algorithm Based on Explosion Gravitation Field Algorithm. ENTROPY 2022;24:e24070873. [PMID: 35885095 PMCID: PMC9322764 DOI: 10.3390/e24070873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023]
22
Xing X, Yang F, Li H, Zhang J, Zhao Y, Gao M, Huang J, Yao J. Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis. Bioinformatics 2022;38:2178-2186. [PMID: 35157021 DOI: 10.1093/bioinformatics/btac088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 02/03/2023]  Open
23
Tan K, Huang W, Liu X, Hu J, Dong S. A multi-modal fusion framework based on multi-task correlation learning for cancer prognosis prediction. Artif Intell Med 2022;126:102260. [DOI: 10.1016/j.artmed.2022.102260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
24
Jin Z, Kang J, Yu T. Feature selection and classification over the network with missing node observations. Stat Med 2022;41:1242-1262. [PMID: 34816464 PMCID: PMC9773124 DOI: 10.1002/sim.9267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/14/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022]
25
Zhang Y, Ma Y. Non-negative multi-label feature selection with dynamic graph constraints. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2021.107924] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
26
Li L, Liu ZP. A connected network-regularized logistic regression model for feature selection. APPL INTELL 2022. [DOI: 10.1007/s10489-021-02877-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Zhang Y, Ma Y, Yang X. Multi-label feature selection based on logistic regression and manifold learning. APPL INTELL 2022. [DOI: 10.1007/s10489-021-03008-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
28
Qiao C, Yang L, Shi Y, Fang H, Kang Y. Deep belief networks with self-adaptive sparsity. APPL INTELL 2022. [DOI: 10.1007/s10489-021-02361-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
29
Dynamic subspace dual-graph regularized multi-label feature selection. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2021.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
30
Li C, Gao Z, Su B, Xu G, Lin X. Data analysis methods for defining biomarkers from omics data. Anal Bioanal Chem 2021;414:235-250. [PMID: 34951658 DOI: 10.1007/s00216-021-03813-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 02/01/2023]
31
Yu K, Xie W, Wang L, Zhang S, Li W. Determination of biomarkers from microarray data using graph neural network and spectral clustering. Sci Rep 2021;11:23828. [PMID: 34903818 PMCID: PMC8668890 DOI: 10.1038/s41598-021-03316-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/02/2021] [Indexed: 11/26/2022]  Open
32
Ma W, Su K, Wu H. Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction. Genome Biol 2021;22:264. [PMID: 34503564 PMCID: PMC8427961 DOI: 10.1186/s13059-021-02480-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022]  Open
33
Nguyen ND, Jin T, Wang D. Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. Bioinformatics 2021;37:1772-1775. [PMID: 33031552 PMCID: PMC8289382 DOI: 10.1093/bioinformatics/btaa866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 12/23/2022]  Open
34
Tan K, Huang W, Liu X, Hu J, Dong S. A Hierarchical Graph Convolution Network for Representation Learning of Gene Expression Data. IEEE J Biomed Health Inform 2021;25:3219-3229. [PMID: 33449889 DOI: 10.1109/jbhi.2021.3052008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
35
Wang X, Dong Y, Zheng Y, Chen Y. Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective. J Genet Genomics 2021;48:520-530. [PMID: 34362682 DOI: 10.1016/j.jgg.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
36
Yang H, Zhuang Z, Pan W. A graph convolutional neural network for gene expression data analysis with multiple gene networks. Stat Med 2021;40:5547-5564. [PMID: 34258781 DOI: 10.1002/sim.9140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 04/07/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023]
37
Yang S, Zhu F, Ling X, Liu Q, Zhao P. Intelligent Health Care: Applications of Deep Learning in Computational Medicine. Front Genet 2021;12:607471. [PMID: 33912213 PMCID: PMC8075004 DOI: 10.3389/fgene.2021.607471] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/05/2021] [Indexed: 12/24/2022]  Open
38
Feng J, Jiang L, Li S, Tang J, Wen L. Multi-Omics Data Fusion via a Joint Kernel Learning Model for Cancer Subtype Discovery and Essential Gene Identification. Front Genet 2021;12:647141. [PMID: 33747053 PMCID: PMC7969795 DOI: 10.3389/fgene.2021.647141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/02/2021] [Indexed: 01/17/2023]  Open
39
GVES: machine learning model for identification of prognostic genes with a small dataset. Sci Rep 2021;11:439. [PMID: 33431999 PMCID: PMC7801384 DOI: 10.1038/s41598-020-79889-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022]  Open
40
Liu J, Su R, Zhang J, Wei L. Classification and gene selection of triple-negative breast cancer subtype embedding gene connectivity matrix in deep neural network. Brief Bioinform 2021;22:6067882. [PMID: 33415328 DOI: 10.1093/bib/bbaa395] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/16/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022]  Open
41
Liu T, Huang J, Liao T, Pu R, Liu S, Peng Y. A Hybrid Deep Learning Model for Predicting Molecular Subtypes of Human Breast Cancer Using Multimodal Data. Ing Rech Biomed 2021. [DOI: 10.1016/j.irbm.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
42
Lee S, Lim S, Lee T, Sung I, Kim S. Cancer subtype classification and modeling by pathway attention and propagation. Bioinformatics 2020;36:3818-3824. [PMID: 32207514 DOI: 10.1093/bioinformatics/btaa203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/13/2020] [Accepted: 03/19/2020] [Indexed: 01/04/2023]  Open
43
Kong Y, Yu T. forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction. Bioinformatics 2020;36:3507-3515. [PMID: 32163118 DOI: 10.1093/bioinformatics/btaa164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 02/07/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022]  Open
44
Gallins P, Saghapour E, Zhou YH. Exploring the Limits of Combined Image/'omics Analysis for Non-cancer Histological Phenotypes. Front Genet 2020;11:555886. [PMID: 33193632 PMCID: PMC7644963 DOI: 10.3389/fgene.2020.555886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/09/2020] [Indexed: 11/13/2022]  Open
45
Xu D, Zhang J, Xu H, Zhang Y, Chen W, Gao R, Dehmer M. Multi-scale supervised clustering-based feature selection for tumor classification and identification of biomarkers and targets on genomic data. BMC Genomics 2020;21:650. [PMID: 32962626 PMCID: PMC7510277 DOI: 10.1186/s12864-020-07038-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/30/2020] [Indexed: 12/19/2022]  Open
46
Nakashima S, Nacher JC, Song J, Akutsu T. An Overview of Bioinformatics Methods for Analyzing Autism Spectrum Disorders. Curr Pharm Des 2020;25:4552-4559. [PMID: 31713477 DOI: 10.2174/1381612825666191111154837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
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Hu J, Li Y, Gao W, Zhang P. Robust multi-label feature selection with dual-graph regularization. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2020.106126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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A supervised machine learning-based methodology for analyzing dysregulation in splicing machinery: An application in cancer diagnosis. Artif Intell Med 2020;108:101950. [PMID: 32972670 DOI: 10.1016/j.artmed.2020.101950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023]
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Li J, Ping Y, Li H, Li H, Liu Y, Liu B, Wang Y. Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network. Comput Biol Chem 2020;88:107317. [PMID: 32622180 DOI: 10.1016/j.compbiolchem.2020.107317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/21/2020] [Indexed: 02/04/2023]
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Zhou X, Chai H, Zhao H, Luo CH, Yang Y. Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning-based neural network. Gigascience 2020;9:giaa076. [PMID: 32649756 PMCID: PMC7350980 DOI: 10.1093/gigascience/giaa076] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]  Open
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