ArticleCell reports methods2024
Tracing unknown tumor origins with a biological-pathway-based transformer model.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- TF-GateNet: An Interpretable and Biologically Guided Framework for Primary-Metastatic State Prediction from Somatic Genomic Alterations.Biomolecules · 2026Article
- PathTIGR: A pathway topology-informed graph representation learning framework for immunotherapy response prediction.Science advances · 2026Article
- PathHDNN: a pathway hierarchical-informed deep neural network framework for predicting immunotherapy response and mechanism interpretation.Genome medicine · 2025Article
- Leveraging artificial intelligence and machine learning in kinase inhibitor development: advances, challenges, and future prospects.RSC medicinal chemistry · 2025Review
- Oxidative Stress and Inflammation in Hypoxemic Respiratory Diseases and Their Comorbidities: Molecular Insights and Diagnostic Advances in Chronic Obstructive Pulmonary Disease and Sleep Apnea.Antioxidants (Basel, Switzerland) · 2025Review
- DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile.Briefings in bioinformatics · 2024Article
- PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer of unknown primary (CUP) represents metastatic cancer where the primary site remains unidentified despite standard diagnostic procedures. To determine the tumor origin in such cases, we developed BPformer, a deep learning method integrating the transformer model with prior knowledge of biological pathways. Trained on transcriptomes from 10,410 primary tumors across 32 cancer types, BPformer achieved remarkable accuracy rates of 94%, 92%, and 89% in primary tumors and primary and metastatic sites of metastatic tumors, respectively, surpassing existing methods. Additionally, BPformer was validated in a retrospective study, demonstrating consistency with tumor sites diagnosed through immunohistochemistry and histopathology. Furthermore, BPformer was able to rank pathways based on their contribution to tumor origin identification, which helped to classify oncogenic signaling pathways into those that are highly conservative among different cancers versus those that are highly variable depending on their origins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.