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A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis

Ayush Mishra Anadi Mishra Adarsh Tiwari Uttam Sharma Nikhil Raj

Subject area: Science,Engineering and Technology  ·  Area of research: Multi-modal Learning, Precision Medicine

Abstract

Early cancer diagnosis is critical for improving patient outcomes but is challenged by the disease?s profound heterogeneity. This paper introduces a unified, AI-powered framework that synergistically integrates histopathology, genomics, and proteomics data to enhance early cancer detection. Our architecture features a novel multi-transformer model with dedicated Vision and Genomic Transformers to encode modality-specific features, which are then fused by a cross-modal attention transformer. This intermediate fusion strategy enables the model to learn intricate genotype-phenotype correlations often missed by traditional methods. Validated on cohorts from The Cancer Genome Atlas (TCGA), our framework demonstrates a significant improvement in diagnostic performance over single-modality baselines. We also incorporate Explainable AI (XAI) techniques to ensure model transparency, a crucial step for clinical adoption. The framework serves as both a powerful diagnostic tool and a hypothesis- generation engine, uncovering novel biomarkers from complex multi-modal data and advancing computational pathology and personalized medicine.

Keywords

Multi-Modal Learning, Transformers, Histopathology, Genomics, Proteomics, Explainable AI, Early Cancer Diagnosis

References

[1] K. D. McCombe, S. G. Craig, A. V. Pulsawatdi, et al., “HistoClean: Open-source software for histological image pre-processing and aug- mentation to improve development of robust convolutional neural net- works,” Computational and Structural Biotechnology Journal, vol. 19, pp. 4840–4853, 2021.

[2] S. S. Band, A. Yarahmadi, C.-C. Hsu, et al., “Application of explain- able artificial intelligence in medical health: A systematic review of interpretability methods,” Informatics in Medicine Unlocked, vol. 40, p. 101286, 2023.

[3] X. Li, M. Li, P. Yan, et al., “Deep Learning Attention Mechanism in Medical Image Analysis: Basics and Beyonds,” International Journal of Network Dynamics and Intelligence, vol. 2, no. 1, pp. 93–116, 2023.

[4] Z. Zhou, X. Feng, L. Huang, et al., “From Hypothesis to Publication: A Comprehensive Survey of AI-Driven Research Support Systems,” arXiv preprint arXiv:2503.01424, 2025.

[5] D. Wilimitis and C. G. Walsh, “Practical Considerations and Applied Examples of Cross-Validation for Model Development and Evaluation in Health Care: Tutorial,” JMIR AI, vol. 2, p. e49023, 2023.

[6] J.-K. He´riche´, S. Alexander, and J. Ellenberg, “Integrating Imaging and Omics: Computational Methods and Challenges,” Annual Review of Biomedical Data Science, vol. 2, pp. 175–197, 2019.

[7] C.-H. Liu, C.-F. Tsai, K.-L. Sue, and M.-W. Huang, “The Feature Selection Effect on Missing Value Imputation of Medical Datasets,” Applied Sciences, vol. 10, no. 7, p. 2344, 2020.

[8] L. Nolte and S. Tomforde, “A Helping Hand: A Survey About AI-Driven Experimental Design for Accelerating Scientific Research,” Applied Sciences, vol. 15, no. 9, p. 5208, 2025.

[9] Z. Zhang, H. Li, S. Jiang, et al., “A survey and evaluation of Web- based tools/databases for variant analysis of TCGA data,” Briefings in Bioinformatics, vol. 20, no. 4, pp. 1524–1541, 2019.

[10] Y. Xu, G. Wu, J. Li, et al., “Screening and Identification of Key Biomarkers for Bladder Cancer: A Study Based on TCGA and GEO Data,” BioMed Research International, vol. 2020, Article ID 8283401, 2020.

[11] S. Kakarmath, A. Esteva, R. Arnaout, et al., “Best practices for authors of healthcare-related artificial intelligence manuscripts,” npj Digital Medicine, vol. 3, no. 1, p. 134, 2020.

[12] C. Meldrum, M. A. Doyle, and R. W. Tothill, “Next-Generation Se- quencing for Cancer Diagnostics: a Practical Perspective,” Clinical Biochemist Reviews, vol. 32, no. 4, pp. 177–195, 2011.

[13] A. M. Hasan, H. A. Jalab, F. Meziane, H. Kahtan, and A. S. Al-Ahmad, “Combining Deep and Handcrafted Image Features for MRI Brain Scan Classification,” IEEE Access, vol. 7, pp. 79959–79967, 2019.

[14] B. Smith, M. Hermsen, E. Lesser, D. Ravichandar, and W. Kremers, “Developing image analysis pipelines of whole-slide images: Pre- and post-processing,” Journal of Clinical and Translational Science, vol. 5, p. e38, 2020.

[15] A. Englisz, M. Smycz-Kuban´ska, and A. Mielczarek-Palacz, “Sensitivity and Specificity of Selected Biomarkers and Their Combinations in the Diagnosis of Ovarian Cancer,” Diagnostics, vol. 14, no. 9, p. 949, 2024.

[16] K. Shah, K. Leow, A. Janssen, T. Shaw, C. Stewart, and I. Kerridge, “Ethical and legal considerations governing use of health data for quality improvement and performance management: a scoping review of the perspectives of health professionals and administrators,” BMJ Open Quality, vol. 14, p. e003309, 2025.

[17] Y. Zhao, R. Gulati, J. Lange, et al., “Sensitivity Measures in Studies of Cancer Early Detection Biomarkers,” Supplementary Materials and Methods, pp. 1–5.

[18] D. Gao, K. Li, R. Wang, S. Shan, and X. Chen, “Multi-Modal Graph Neural Network for Joint Reasoning on Vision and Scene Text,” in Proceedings of the IEEE International Conference on Computer Vision (ICCV), 2019, pp. 12746–12756.

[19] S. M. Raea, K. M. Almotairi, A. M. Alharbi, et al., “Ethical consider- ations in the use of patient medical records for research,” International Journal of Health Sciences, vol. 7, no. S1, pp. 3829–3841, 2023.

[20] C. O. Dumitru and M. Datcu, “Information Content of Very High Resolution SAR Images: Study of Feature Extraction and Imaging Parameters,” IEEE Transactions on Geoscience and Remote Sensing, vol. 51, no. 8, pp. 4591–4610, 2013.

[21] V. W. Lumumba, D. Kiprotich, M. L. Mpaine, N. G. Makena, and M. D. Kavita, “Comparative Analysis of Cross-Validation Tech- niques: LOOCV, K-folds Cross-Validation, and Repeated K-folds Cross- Validation in Machine Learning Models,” American Journal of Theoret- ical and Applied Statistics, vol. 13, no. 5, pp. 127–137, 2024.

[22] M. Ennab and H. Mcheick, “Advancing AI Interpretability in Medical Imaging: A Comparative Analysis of Pixel-Level Interpretability and Grad-CAM Models,” Machine Learning and Knowledge Extraction, vol. 7, no. 1, p. 12, 2025.

[23] R. Vuokko, A. Vakkuri, and S. Palojoki, “Systematized Nomenclature of Medicine–Clinical Terminology (SNOMED CT) Clinical Use Cases in the Context of Electronic Health Record Systems: Systematic Literature Review,” JMIR Medical Informatics, vol. 11, p. e43750, 2023.

[24] M. Mann, C. Kumar, W.-F. Zeng, and M. T. Strauss, “Artificial intelli- gence for proteomics and biomarker discovery,” Cell Systems, vol. 12, pp. 759–770, 2021.

[25] M. Adnan, S. Kalra, J. C. Cresswell, G. W. Taylor, and H. R. Tizhoosh, “Federated learning and differential privacy for medical image analysis,” Scientific Reports, vol. 12, no. 1, p. 1953, 2022.

[26] Y. Chen, et al., “UMPSNet: A Unified Model for Multi-cancer Prog- nostic Survey across Multiple Pathological Slides,” arXiv preprint arXiv:2401.07016, 2024.

[27] S. Rasool, “Integrative Relational Learning on Multimodal Oncology Data,” Moffitt Cancer Center Research, 2024.

[28] Y. Xu, et al., “MUFASA: Multimodal Fusion Architecture Search for Electronic Health Records,” in Proceedings of the AAAI Conference on Artificial Intelligence, vol. 35, no. 12, pp. 10532–10540, 2021.

[29] A. Sharma, et al., “Systematic Review of Hybrid Vision Transformer Architectures for Radiological Image Analysis,” Journal of Imaging Informatics in Medicine, 2025.

[30] M. Maillard, et al., “KD-Net: A Knowledge Distillation framework for multi-modal to mono-modal segmentation,” in International Conference on Medical Image Computing and Computer-Assisted Intervention, 2020, pp. 38–47.

[31] J. Chen, et al., “Fair Machine Learning in Healthcare: A Review,” ACM Computing Surveys, vol. 55, no. 1, pp. 1–38, 2022.

[32] S. Pfohl, et al., “On the fairness of machine learning in healthcare: dataset shifts and mitigation,” Nature Communications, vol. 14, no. 1, p. 7093, 2023.

How to cite this paper

Ayush Mishra, Anadi Mishra, Adarsh Tiwari, Uttam Sharma, Nikhil Raj "A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis" Iconic Research And Engineering Journals Volume 9 Issue 5 2025 Page 197-205
Ayush Mishra, Anadi Mishra, Adarsh Tiwari, Uttam Sharma, Nikhil Raj "A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis" Iconic Research And Engineering Journals, vol. 9, no. 5, Nov. 2025
Ayush Mishra, Anadi Mishra, Adarsh Tiwari, Uttam Sharma, Nikhil Raj (2025). A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis. Iconic Research And Engineering Journals, 9(5).
Ayush Mishra, Anadi Mishra, Adarsh Tiwari, Uttam Sharma, Nikhil Raj "A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis" Iconic Research And Engineering Journals, vol. 9, no. 5, Nov. 2025.
@article{1711765,
      author = {Ayush Mishra, Anadi Mishra, Adarsh Tiwari, Uttam Sharma, Nikhil Raj},
      title = {A Unified Multi-Modal Transformer Framework for Synergistic Cancer Diagnosis},
      journal = {Iconic Research And Engineering Journals},
      year = {2025},
      volume = {9},
      number = {5},
      pages = {197-205},
      issn = {2456-8880},
      url = {https://www.irejournals.com/formatedpaper/1711765.pdf},
      abstract = {Early cancer diagnosis is critical for improving patient outcomes but is challenged by the disease?s profound heterogeneity. This paper introduces a unified, AI-powered framework that synergistically integrates histopathology, genomics, and proteomics data to enhance early cancer detection. Our architecture features a novel multi-transformer model with dedicated Vision and Genomic Transformers to encode modality-specific features, which are then fused by a cross-modal attention transformer. This intermediate fusion strategy enables the model to learn intricate genotype-phenotype correlations often missed by traditional methods. Validated on cohorts from The Cancer Genome Atlas (TCGA), our framework demonstrates a significant improvement in diagnostic performance over single-modality baselines. We also incorporate Explainable AI (XAI) techniques to ensure model transparency, a crucial step for clinical adoption. The framework serves as both a powerful diagnostic tool and a hypothesis- generation engine, uncovering novel biomarkers from complex multi-modal data and advancing computational pathology and personalized medicine.},
      keywords = {Multi-Modal Learning, Transformers, Histopathology, Genomics, Proteomics, Explainable AI, Early Cancer Diagnosis},
      month = {November},
  }