Table 1 Methods summary
From: Deep learning-based approaches for multi-omics data integration and analysis
Method | Model architecture | Data source | Modalities handled | Handles incomplete data | Task |
|---|---|---|---|---|---|
MOLI [16] | FNN | somatic mutation, CNV, gene expression | No | drug response prediction | |
SNN [17] | FNN | TCGA [67] | gene expression, DNA methylation | No | classification |
GLUER [18] | FNN | self-generated [18] | single-cell gene expression and epigenomics, spatial transcriptomics | Yes | matching cells across different single-cell data modalities |
CapsNetMMD [19] | FNN | TCGA [67] | gene expression, DNA methylation, CNV | No | phenotype-related gene identification |
MOMA [20] | FNN | gene expression, DNA methylation | No | classification | |
SALMON [21] | FNN | TCGA [67] | gene expression, miRNA expression | No | survival prediction |
MiNet [22] | FNN | gene expression, CNV, DNA methylation, biological pathways | No | survival prediction | |
DeepOmix [23] | FNN | genomics, CNV, gene expression, DNA methylation, biological pathways | No | survival prediction | |
MOGONET [10] | GCN | gene expression, miRNA expression, DNA methylation | No | classification | |
MoGCN [24] | GCN | TCGA [67] | somatic mutation, gene expression, proteomics | No | classification |
MOFGCN [25] | GCN | gene expression, CNV, somatic mutation, drug-cell line associations | No | drug response prediction | |
AGCN [26] | GCN | gene expression, CNV, DNA methylation, PPI network | No | classification | |
DeepMOCCA [27] | GCN | somatic mutation, DNA methylation, gene expression, CNV, PPI network | No | survival prediction | |
Chaudhary et al. [28] | AE | TCGA [67] | gene expression, miRNA expression, DNA methylation | No | dimensionality reduction; clustering |
Zhang et al. [29] | AE | gene expression, CNV | No | dimensionality reduction; clustering | |
Song et al. [30] | AE | TCGA [67] | DNA methylation, gene expression, miRNA expression | No | dimensionality reduction; clustering |
DeepAutoGlioma [31] | AE | TCGA [67] | gene expression, DNA methylation | No | dimensionality reduction; clustering |
DRIM [32] | AE | CCLE [71] | gene expression, CNV, DNA methylation, genomics | No | drug response prediction and analysis |
AE+consensus learning [33] | AE | TCGA [67] | gene expression, DNA methylation, miRNA expression, CNV | No | survival prediction |
concatAE/crossAE [34] | AE | TCGA [67] | gene expression, DNA methylation, miRNA expression, CNV | No | survival prediction |
MOCSS [35] | AE | TCGA [67] | gene expression, miRNA expression, DNA methylation | No | clustering |
DLSF [36] | AE | TCGA [67] | gene expression, DNA methylation, miRNA expression | No | clustering |
MultiGATAE [37] | AE | TCGA [67] | miRNA expression, gene expression, DNA methylation | No | clustering |
MAE [38] | AE | gene expression, miRNA expression, proteomics, DNA methylation, molecular interaction networks, | No | classification | |
MvNE [39] | Variational | TCGA [67] | gene expression, miRNA expression, DNA methylation | Yes | representation learning; clustering |
DCCA [40] | VAE | 10X Genomics [76] | paired single-cell transcriptomics and single-cell epigenomics | Yes | representation learning; clustering; regulatory inference |
Multigrate [41] | VAE | 10X Genomics [76] | single-cell transcriptomics, single-cell epigenomics, single-cell proteomics | Yes | multimodal data integration and imputation; multimodal atlas construction |
GLUE [42] | VAE | SNARE-seq [77], SHARE-seq [78], 10X Multiome [76], Nephron [79], MOp [80] | scRNA-seq, snmC-seq, scATAC-seq | Yes | multi-modal data integration; regulatory inference; multi-omics atlas construction |
LSTM-VAE [43] | VAE | Lau et al. [81] | temporal proteomics and metabolomics | No | clustering |
CVAE [44] | VAE | TCGA [67] | mRNA, DNA methylation, microRNA | No | classification |
OmiVAE [45] | VAE | TCGA [67] | gene expression, DNA methylation | No | classification |
MMD-VAE [46] | VAE | TCGA [67] | CNV, mRNA, RNAseq, DNA methylation | No | clustering; classification; survival analysis |
OmiEmbed [47] | VAE | gene expression, DNA methylation, miRNA expression | No | multi-task: classification, regression, survival prediction | |
DeepIMV [48] | Variational (encoder only) | mRNA expressions, DNA methylation, microRNA expressions, reverse phase protein array, DNA copy number, metabolites | Yes | classification | |
Subtype-GAN [49] | GAN | TCGA [67] | CNA, mRNA, miRNA, DNA methylation | No | clustering |
omicsGAN [50] | GAN | mRNA expression, miRNA expression, miRNA-mRNA interaction network | No | classification | |
CLUE [51] | VAE+GAN | single-cell gene expression, single-cell proteomics, single-cell epigenomics | Yes | multimodal single-cell integration | |
scGPT [52] | GPT | single-cell transcriptomics, single-cell epigenomics, single-cell proteomics | Yes | foundation model; diverse tasks: cell type annotation, multi-batch integration, multi-omic integration, perturbation response prediction, gene network inference | |
Carrillo-Perez et al. [53] | CNN+SVM + late fusion | TCGA [67] | pathomics, gene expression, miRNA expression, CNV, DNA Methylation | No | classification |
Chen et al. [54] | AE + late fusion | TCIA NSCLC [86] | radiomics, gene expression, clinical | No | survival prediction |
Pathomic Fusion [55] | CNN+FNN+ attention | TCGA [67] | pathomics, genomics, CNV, gene expression | No | survival prediction |
Shirkavand et al. [56] | transformer + GAN | radiomics, genomics | Yes | regression; classification | |
JSRL [57] | GAN | radiomics (MRI+PET) | Yes | classification | |
Tulder and Bruijne [58] | CNN | radiomics (multiple MRI modalities) | Yes | classification | |
Morar et al. [59] | FNN | ADNI [87] | radiomics (MRI, PET), biospecimen (CSF), cognitive scores | No | regression |
MildInt [60] | RNN | ADNI [87] | radiomics, longitudinal cognitive scores, biospecimen (CSF) | No | classification |
Xu et al. [61] | RNN | ADNI [87] | longitudinal radiomics (MRI, PET), demographics | Yes | regression; trajectory prediction |
MCNetWang et al. [62] | RNN | longitudinal radiomics (MRI, PET) | Yes | classification | |
LSN [63] | FNN | longitudinal radiomics (MRI), genetics, clinical | No | classification |