Machine learning and multi-omics integration: advancing cardiovascular translational research and clinical practice

Table 3 ML models for treatment strategies in CVDs

Category	Function	Method	Data type	Code availability	Refs
Drug & Target Discovery	Candidate Target Discovery	Integration	Transcriptomics	https://huggingface.co/ctheodoris/Geneformer	[70]
	Candidate Target Discovery	ANN	Multi-omics	https://www.mdpi.com/article/10.3390/cells10123268/s1	[71]
	Finding Drugs	CNN, GRU	Proteomics	http://ahtps.zhanglab.site/	[72]
Drug & Target Validation	Drug Repurposing Predictions	Integration	Multi-omics	https://github.com/NCATSTranslator/Translator-All/wiki/Molecular-Data-Provider	[73]
	Drug-target Interaction Validation	LASSO, RF	Proteomics	https://github.com/QUST-AIBBDRC/LRF-DTIs/	[74]
	Drug-target Interaction Validation	Integration	Multi-omics	http://120.77.11.78/DeepMPF/	[75]
Efficacy & Side Effects	Efficacy Verification	Integration	Genomic	–	[76]
	Efficacy Verification	FNN, SVM	Transcriptomics	–	[77]
	Efficacy Verification	Integration	Genomic	https://www.hgsc.bcm.edu/software	[78]
	Prediction of Drug Side Effects	Integration	Transcriptomics	https://github.com/vauyeung38/sct-transcriptomics-waveforms	[79]
	Prediction of Drug Side Effects	Integration	Proteomics	http://github.com/yuliyi/MSDSE	[81]
	Prediction of Drug Side Effects	CNN, MLP	Multi-omics	http://github.com/OnurUner/DeepSide	[82]
	Drug Sensitivity Prediction	GNN	Multi-omics	https://github.com/kkkayle/GCFMCL	[83]
	Optimization of Drugs	Integration	Multi-omics	https://github.com/dahjan/DMS_opt	[84]

ANN, Artificial Neural Network; CNN, Convolutional Neural Network; GRU, Gated Recurrent Unit; KNN, K-nearest Neighbors; LASSO, Least Absolute Shrinkage and Selection Operator; RF, Random Forest; DNN, Deep Neural Network; FNN, Feedforward Neural Network; SVM, Support Vector Machine; GNN, Graph Neural Network; MLP, Multilayer Perceptron

ISSN: 1479-5876