Table 1.

Summary of AI methods in breast cancer immunotherapy prediction

Omic	Biomarker	Task	Data source	Tumor	Model/Algorithm	Year	Reference
Transcriptomic	Expression of M2-like tumour-associated macrophages	Immunotherapy response	TCGA	TNBC	Simple neural network-based deep learning	2020	Bao et al. 2020)
	Expression of antigen processing and presentation machinery	Prognostic	TCGA	BC	LASSO logistic regression and RF	2023	Müller et al. 2023)
	Expression of costimulatory molecule genes	TIME status	TCGA	TNBC	LASSO and SVM-RFE	2024	Zhang et al. 2024)
	Expression of genes	Immune-related cells	Institutional and public Dataset	BC and melanoma	Gaussian mixture modeling, Kullback–Leibler (KL) divergence, and mutual nearest-neighbors criteria	2023	Zou et al. 2023)
	Expression of redox-related gene	Prognostic	Institutional and public dataset	BC	RF, LASSO, GBM, Survival-SVM, superpc, Ridge Regression, plsrcox, coxboost, Stepwise Cox regression, and Enet	2024	Wang et al. 2024)
	Expression of genes	pCR	Institutional and public dataset	BC	LASSO, SVM-RFE, and xgboost	2024	Lu et al. 2024)
	Expression of DPP4-related genes	Prognosis	Institutional and public dataset	TNBC	Xgboost, RF, adaboost, KNN, ANN, and LR	2023	Kang et al. 2023)
Proteomic	IHC and H&E TMA	PD-L1 expression	Public dataset	Breast cancer	CNN model with residual connections	2022	Shamai et al. 2022)
	IHC images	PD-L1 Status	Institutional dataset	Pan-cancer	Weakly supervised deep learning with ResNet-50 and attention-based MIL	2024	Ligero et al. 2024)
	Expression of signature proteins	Immunotherapy response	Institutional dataset	TNBC	RF	2024	Li et al. 2024)
Pathology	H&E WSI	Prognostic	Institutional and TCGA dataset	TNBC	Dual CNN	2022	Zhao et al. 2022)
	WSI	TIL	Clinical studies and TCGA datasets	BC	CNN architectures with segmentation and attention-based classifier	2024	Perera et al. 2024)
	WSI	Immunotherapy-related gene	TCGA	BC	MIL architecture with resnet-18	2025	Zhang et al. 2025)
	H&E TMA	pCR	Clinical studies	TNBC	Regularized logistic regression	2023	Wang et al. 2023a)
	H&E WSI	lncRNA–metabolism class prediction	Institutional and TCGA dataset	BC	Resnet50 for feature extraction and gated attention	2024	Yu et al. 2024)
	H&E WSI	TMB	TCGA	TNBC	LR, KNN, RF, and DT	2025	Bendani et al. 2025)
	H&E WSI	TIL and ki-67	Public dataset	BC	U-net-like backbone with CNN and residual dilated inception module	2021	Negahbani et al. 2021)
Radiomic	DEC-MRI	pCR	Institutional dataset	TNBC	Lasso regression	2023	Ramtohul et al. 2024)
	DCE-MRI	TME subtypes	TCGA	BC	RF	2024	Han et al. 2024)
	CE-CT	Immunotherapy response	Clinical studies	BC	Multivariable logistic regression	2023	Zhao et al. 2023)
	MRI	TIL	Institutional dataset	BC	LR, RF, MLP, SVM, LDA, and GB	2022	Huang and Lin 2022)
	PET/CT	pCR	Institutional dataset	TNBC	LR	2023	Seban et al. 2023)
Epigenetic	Methylation level of CpG sites	Prognostic	TCGA	BC	Cox and LASSO regression	2021	Zhang et al. 2021)
	Expression of senescence-relevant lncRNAs	Prognostic	TCGA	BC	Cox and LASSO regression	2023	Yu et al. 2023b)
	Expression of nine hub lncRNAs	CD8 T-cell levels	TCGA	BC	DT, GBM, GLM, ANN, RF, SVM	2022	Chen et al. 2022b)
	Expression of Mitochondrial DNA methylation	Prognostic	TCGA	BC	Cox and LASSO regression	2023	Ma et al. 2023)
Microbiology	Abundances of microbe	Prognostic	TCGA	BC	Cox and LASSO regression	2021	Mao et al. 2022)
	Genus-level intratumor microbiome	Prognostic	TCGA	BC	Cox and LASSO regression	2024	Li et al. 2024)
Omic	256 multi-modal biomarker signatures from (gene expression, cellular morphometric biomarkers, and abundance of microbe)	Prognostic	TCGA	BC	Multivariate Cox regression	2022	Mao et al. 2022)
	Radiological features and gene expression	Axillary lymph node metastasis	TCGA	BC	Multivariate LR analysis	2024	Lai et al. 2024)
	Pathology images, lncRNA data, immune cell scores, and clinical features	Prognostic	Institutional and TCGA dataset	BC	CNN architecture with attention-module, concatenation fusion, and a conclusive regressor	2024	Yu et al. 2024)
	Mammogram, MRI, radiological, histopathological, personal, and clinical data	Pcr	Institutional and public Dataset	BC	Resnet18 architecture for feature extraction, cross-modal knowledge mining, and ensemble model for final prediction	2024	Gao et al. 2024)
Genomic	RNA-seq data	Somatic copy number aberrations	TCGA	Pan-cancer	Sequence models and graph neural networks	2024	2024)
	Whole-exome sequencing and RNA sequencing	Neoantigen immunogenicity	Institutional dataset	Pan-cancer	Ensemble model (LR and xgboost)	2023	Jin et al. 2021)
	Genomic instability-related lncRNA signature	Prognostic	TCGA	BC	Multivariate Cox regression	2022	Jiao et al. 2022)

TCGA The cancer genome atlas, TNBC Triple-negative breast cancer, BC Breast cancer, LASSO Least absolute shrinkage and selection operator, RF Random forest, SVM-RFE Support vector machine-recursive feature elimination, GBM Gradient boosting machines, SuperPC Supervised principal component, plsRcox partial least squares cox regression,Enet Elastic net, xgBoost extreme gradient boosting, AdaBoost Adaptive boosting, KNN K-nearest neighbor, ANN Artificial neural networks, LR Logistic regression, DT Decision tree, MLP Multilayer perceptron, LDA Linear discriminant analysis, GB Gradient boosting, GLM Generalized linear models, CNN Convolutional neural network, MIL Multiple instance learning, xgBoost extreme gradient boosting, IHC Immunohistochemistry, H&E Hematoxylin and eosin, TMA Tissue microarray, pCR pathological complete response, DPP4 dipeptidyl peptidase 4, TIL Tumor-infiltrating lymphocytes, TME Tumor microenvironment, DCE-MRI Dynamic contrast-enhanced MRI, CT Computed tomography, PET Positron emission tomography, WSI Whole slide imaging, TMB Tumor mutation burden, lncRNA long non-coding RNA