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References from Pathway-guided architectures for interpretable AI in biological research. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1146/annurev-pathol-020712-163923
10.1146/annurev-pathol-020712-163923 · External reference
Integration of deep learning-based image analysis and genomic data in cancer pathology: a systematic review
10.1016/j.ejca.2021.10.007 · 2022 · External reference
A review of the application of deep learning in medical image classification and segmentation
10.21037/atm.2020.02.44 · 2020 · External reference
10.1098/rsif.2017.0387
10.1098/rsif.2017.0387 · External reference
Artificial intelligence and machine learning in predicting the response to immunotherapy in non-small cell lung carcinoma: a systematic review
2024 · External reference
10.1093/nar/gkw1092
10.1093/nar/gkw1092 · External reference
The Gene Ontology (GO) database and informatics resource
2004 · External reference
10.1093/nar/gkad1025
10.1093/nar/gkad1025 · External reference
10.1093/bioinformatics/btr260
10.1093/bioinformatics/btr260 · External reference
DeepCC: a novel deep learning-based framework for cancer molecular subtype classification
10.1038/s41389-019-0157-8 · 2019 · External reference
10.1038/nmeth.4627
10.1038/nmeth.4627 · External reference
A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data
10.1186/s12859-023-05262-8 · 2023 · External reference
Strategies to include prior knowledge in omics analysis with deep neural networks
10.1016/j.patter.2025.101203 · 2025 · External reference
10.1109/access.2024.3409843
10.1109/access.2024.3409843 · External reference
Towards an interpretable deep learning model of cancer
10.1038/s41698-025-00822-y · 2025 · External reference
Unresolved reference
2024 · External reference
10.1093/bioinformatics/btae257
10.1093/bioinformatics/btae257 · External reference
GenNet framework
10.1038/s42003-021-02622-z · 2021 · External reference
A deep neural network for gastric cancer prognosis prediction based on biological information pathways
2022 · External reference
IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability
10.1093/bib/bbae080 · 2024 · External reference
10.1097/cji.0000000000000475
10.1097/cji.0000000000000475 · External reference
GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway–pathway interaction network
10.1093/bioinformatics/btae165 · 2024 · External reference
10.1038/s41586-021-03922-4
10.1038/s41586-021-03922-4 · External reference
10.5220/0012420700003657
10.5220/0012420700003657 · External reference
Optimized Graph neural network-multilayer perceptron fusion classifier for metastatic prostate cancer detection in Western and Asian populations
2025 · External reference
PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation
10.1093/bib/bbae497 · 2024 · External reference
Biologically informed deep learning for explainable epigenetic clocks
10.1038/s41598-023-50495-5 · 2024 · External reference
scGO: interpretable deep neural network for cell status annotation and disease diagnosis
10.1093/bib/bbaf018 · 2025 · External reference
Transparent sparse graph pathway network for analyzing the internal relationship of lung cancer
10.3389/fgene.2024.1437174 · 2024 · External reference
Quantitative Mass Spectrometry-Based Proteomics: An Overview
10.1007/978-1-0716-1024-4_8 · 2021 · External reference
Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium
10.1158/2159-8290.cd-13-0219 · 2013 · External reference
Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis
10.1038/s41467-023-41146-4 · 2023 · External reference
Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics
10.1021/pr501138h · 2015 · External reference
10.1038/s41592-021-01197-1
10.1038/s41592-021-01197-1 · External reference
Exploring Mechanisms and Biomarkers of Breast Cancer Invasion and Migration: an Explainable Gene-Pathway-Compounds Neural Network
10.1002/cam4.70769 · 2025 · External reference
c-Diadem: a constrained dual-input deep learning model to identify novel biomarkers in Alzheimer's disease
10.1186/s12920-023-01675-9 · 2023 · External reference
Using interpretable deep learning to model cancer dependencies
10.1093/bioinformatics/btab137 · 2021 · External reference
10.1093/bioinformatics/btac636
10.1093/bioinformatics/btac636 · External reference
MULGONET: An interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery
2025 · External reference
10.1016/j.csbj.2021.04.067
10.1016/j.csbj.2021.04.067 · External reference
MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis
10.1093/bioinformatics/btae362 · 2024 · External reference
10.1016/j.csbj.2023.09.021 · Admitted local publication
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data
2024 · External reference
A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions
10.1038/s41467-025-56475-9 · 2025 · External reference
10.1016/j.isci.2022.103798
10.1016/j.isci.2022.103798 · External reference
10.1101/2024.11.19.24317595
10.1101/2024.11.19.24317595 · External reference
10.1093/nar/gkac988
10.1093/nar/gkac988 · External reference
10.1016/j.csbj.2024.07.019 · Admitted local publication
Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data
10.1186/s12920-019-0624-2 · 2019 · External reference
Risk stratification and pathway analysis based on graph neural network and interpretable algorithm
10.1186/s12859-022-04950-1 · 2022 · External reference
10.1145/3698587.3701397
10.1145/3698587.3701397 · External reference
Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration
2024 · External reference
Combining clinical embeddings with multi-omic features for improved patient classification and interpretability in Parkinson’s Disease
2025 · External reference
10.1016/j.ccell.2020.09.014
10.1016/j.ccell.2020.09.014 · External reference
ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways
10.1093/nargab/lqab097 · 2021 · External reference
10.1021/c160017a018
10.1021/c160017a018 · External reference
Knowledge graph aids comprehensive explanation of drug and chemical toxicity
10.1002/psp4.12975 · 2023 · External reference
10.1016/j.patter.2022.100565
10.1016/j.patter.2022.100565 · External reference
XMR: an explainable multimodal neural network for drug response prediction
10.3389/fbinf.2023.1164482 · 2023 · External reference
PathSynergy: a deep learning model for predicting drug synergy in liver cancer
2025 · External reference
Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network
2024 · External reference
arXiv preprint
2020 · External reference
Swin transformer: Hierarchical vision transformer using shifted windows
2021 · External reference
Unresolved reference
2024 · External reference
Unresolved reference
External reference
10.1109/cvpr52733.2024.01100
10.1109/cvpr52733.2024.01100 · External reference
10.1038/s41586-019-1103-9
10.1038/s41586-019-1103-9 · External reference
Explainable deep learning for identifying cancer driver genes based on the Cancer Dependency Map
2025 · External reference
Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
10.1093/database/bau126 · 2015 · External reference
10.1093/bioinformatics/btn577
10.1093/bioinformatics/btn577 · External reference
Pathway enrichment analysis approach based on topological structure and updated annotation of pathway
10.1093/bib/bbx091 · 2019 · External reference
Gene set analysis exploiting the topology of a pathway
10.1186/1752-0509-4-121 · 2010 · External reference
10.1093/bioinformatics/btl140
10.1093/bioinformatics/btl140 · External reference
Pathway Commons, a web resource for biological pathway data
10.1093/nar/gkq1039 · 2010 · External reference
10.1093/nar/gkn653
10.1093/nar/gkn653 · External reference
The BioGRID interaction database: 2008 update
10.1093/nar/gkm1001 · 2007 · External reference
Author Correction: A census of pathway maps in cancer systems biology
10.1038/s41568-021-00331-7 · 2021 · External reference
SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types
10.3390/biology12040579 · 2023 · External reference
PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas
10.1093/bioinformatics/btad684 · 2023 · External reference
Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity
10.1021/acs.jcim.0c00331 · 2020 · External reference
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model
10.1186/s12859-020-03850-6 · 2021 · External reference
Predicting Anticancer Drug Response With Deep Learning Constrained by Signaling Pathways
10.3389/fbinf.2021.639349 · 2021 · External reference
Microbial gene ontology informed deep neural network for microbe functionality discovery in human diseases
10.1371/journal.pone.0290307 · 2023 · External reference
PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery
10.1186/s12859-023-05535-2 · 2023 · External reference
10.3390/biom14121501
10.3390/biom14121501 · External reference
MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model
10.1093/bioinformatics/btad432 · 2023 · External reference
An interpretable artificial intelligence framework for designing synthetic lethality-based anti-cancer combination therapies
10.1016/j.jare.2023.11.035 · 2024 · External reference
GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression
10.1093/bioinformatics/btac147 · 2022 · External reference
SPIN: sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis
10.1093/bib/bbae239 · 2024 · External reference
IRnet: immunotherapy response prediction using pathway knowledge-informed graph neural network
2024 · External reference
10.1016/j.patter.2023.100758
10.1016/j.patter.2023.100758 · External reference
DRPreter: interpretable anticancer drug response prediction using knowledge-guided graph neural networks and transformer
10.3390/ijms232213919 · 2022 · External reference
Decoding cell identity with multi-scale explainable deep learning
2024 · External reference
Unresolved reference
External reference
DeePathNet: a transformer-based deep learning model integrating multiomic data with cancer pathways
10.1158/2767-9764.crc-24-0285 · 2024 · External reference
10.1109/tmi.2020.3021387
10.1109/tmi.2020.3021387 · External reference
Deep-LIFT: Deep label-specific feature learning for image annotation
10.1109/tcyb.2021.3049630 · 2021 · External reference
A unified approach to interpreting model predictions
2017 · External reference
Unresolved reference
2017 · External reference
Grad-cam: Visual explanations from deep networks via gradient-based localization
2017 · External reference
Unresolved reference
External reference
10.1371/journal.pone.0130140
10.1371/journal.pone.0130140 · External reference
Gnnexplainer: Generating explanations for graph neural networks
2019 · External reference
XAI-based data visualization in multimodal medical data
2025 · External reference
arXiv preprint
2025 · External reference
Explainable artificial intelligence in drug discovery: bridging predictive power and mechanistic insight
10.1002/wcms.70049 · 2025 · External reference
Explainable artificial intelligence for medical imaging systems using deep learning: a comprehensive review
10.1007/s10586-025-05281-5 · 2025 · External reference
A comparative analysis of DNN-based white-box explainable AI methods in network security
10.1186/s13635-025-00201-x · 2025 · External reference
PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data
10.1186/s12859-018-2500-z · 2018 · External reference
10.1109/sds60720.2024.00044
10.1109/sds60720.2024.00044 · External reference
10.1038/s41467-023-35923-4
10.1038/s41467-023-35923-4 · External reference
VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics
10.1038/s41467-021-26017-0 · 2021 · External reference
PAUSE: principled feature attribution for unsupervised gene expression analysis
10.1186/s13059-023-02901-4 · 2023 · External reference
10.1021/acsomega.2c06659
10.1021/acsomega.2c06659 · External reference
10.1038/s41467-023-40271-4
10.1038/s41467-023-40271-4 · External reference
Graph deep learning enabled spatial domains identification for spatial transcriptomics
2023 · External reference
10.1093/bioinformatics/btz682
10.1093/bioinformatics/btz682 · External reference
10.1126/sciadv.abj7176
10.1126/sciadv.abj7176 · External reference
Unresolved reference
2010 · External reference
Unresolved reference
External reference
Cancer subtype classification and modeling by pathway attention and propagation
10.1093/bioinformatics/btaa203 · 2020 · External reference
10.1038/s41514-021-00068-5
10.1038/s41514-021-00068-5 · External reference
PmVAE: Learning interpretable single-cell representations with pathway modules
2021 · External reference
Classification and functional analysis between cancer and normal tissues using explainable pathway deep learning through RNA-sequencing gene expression
10.3390/ijms222111531 · 2021 · External reference
Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge
10.1093/bib/bbae314 · 2024 · External reference
CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data
2023 · External reference
ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction
10.1093/bioinformatics/btad679 · 2023 · External reference
BDKANN - Biological Domain Knowledge-based Artificial Neural Network for drug response prediction
2020 · External reference
Explainable drug side effect prediction via biologically informed graph neural network
2023 · External reference
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data
10.1038/s41540-024-00405-w · 2024 · External reference
Interpretable deep learning for improving cancer patient survival based on personal transcriptomes
10.1038/s41598-023-38429-7 · 2023 · External reference
10.1016/j.compbiomed.2023.107117
10.1016/j.compbiomed.2023.107117 · External reference
BioXNet: a biologically inspired neural network for deciphering anti-cancer drug response in precision medicine
2024 · External reference
