Table 2.

Machine learning tools for multi-omics data integration

Name	Model	Programming language	API for custom data	Can handle missing values	Publication year	Citations to date	Source code
General-purpose
MOFA2/MOFA (Argelaguet et al., 2018, 2020)	Matrix factorisation	R	Yes	Yes	2020/2018	77/295	https://github.com/bioFAM/MOFA2 https://github.com/bioFAM/MOFA
sCCA (Rodosthenous et al., 2020)	CCA	R	No	No	2020	5	https://github.com/theorod93/sCCA
DIABLO (Singh et al., 2019)	CCA/LDA	R	Yes	Yes	2019	140	http://mixomics.org/
web-rMKL (Speicher and Pfeifer, 2015)	Multi-kernel	Web-interface	Yes	No	2019	1	https://web-rmkl.org/home/upload/
iClusterBayes/iClusterPlus/iCluster (Mo et al., 2013, 2018; Shen et al., 2009)	Bayesian model	R	Yes	No	2018/2013/2009	76/NA/206	https://www.bioconductor.org/packages/devel/bioc/html/iClusterPlus.html
moCluster (Meng et al., 2016)	Bayesian model	R	Yes	No	2016	49	https://www.bioconductor.org/packages/release/bioc/html/mogsa.html
sGCCA (Tenenhaus et al., 2014)	CCA	R	Yes	No	2014	134	https://cran.r-project.org/web/packages/RGCCA/index.html
JIVE (Lock et al., 2013)	Matrix factorisation	R	Yes	No	2013	331	https://cran.r-project.org/src/contrib/Archive/r.jive/
DeepCCA (Andrew et al., 2013)	Deep learning + CCA	Python	No	No	2013	73	https://github.com/VahidooX/DeepCCA
Task-specific
Clustering
NEMO (Rappoport and Shamir, 2019)	Affinity clustering	R	Yes	No	2019	50	https://github.com/Shamir-Lab/NEMO
Similarity Network Fusion (SNF) (Wang et al., 2014)	Network-based	R/MATLAB	Yes	No	2014	980	http://compbio.cs.toronto.edu/SNF/SNF/Software.html
Drug response prediction
MOLI (Sharifi-Noghabi et al., 2019)	Deep learning	Python	No	No	2019	78	https://github.com/hosseinshn/MOLI
CaDRReS (Suphavilai et al., 2018)	Recommender System	Python 2	No	No	2018	49	https://github.com/CSB5/CaDRReS
HNMDRP (Zhang et al., 2018)	Network-based	R/MATLAB	No	No	2018	47	https://github.com/USTC-HIlab/HNMDRP
DRLP (Stanfield et al., 2017)	Network-based	MATLAB	No	No	2017	52	http://compbio.case.edu/omics/software/drlp/index.html