Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data

Maksym Albin Jopek; Krzysztof Pastuszak; Sebastian Cygert; Myron G Best; Thomas Würdinger; Jacek Jassem; Anna Żaczek; Anna Supernat

doi:10.1109/jtehm.2024.3360865

Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data

Abstrakt

The field of cancer diagnostics has been revolutionized by liquid biopsies, which offer a bridge between laboratory research and clinical settings. These tests are less invasive than traditional biopsies and more convenient than routine imaging methods. Liquid biopsies allow studying of tumor-derived markers in bodily fluids, enabling the development of more precise cancer diagnostic tests for screening, disease monitoring, and therapy personalization. This study presents a multiclass approach based on deep learning to analyze and classify diseases based on blood platelet RNA. Its primary objective is to enhance cancer-type diagnosis in clinical settings by leveraging the power of deep learning combined with high-throughput sequencing of liquid biopsy. Ultimately, the study demonstrates the potential of this approach to accurately identify the patient’s type of cancer. Methods: The developed method classifies patients using heatmap images, generated based on gene expression arranged according to the Kyoto Encyclopedia of Genes and Genomes pathways. The images represent samples of patients with ovarian cancer, endometrial cancer, glioblastoma, non-small cell lung cancer, and sarcoma, as well as cancer patients with brain metastasis. Results: Our deep learning-based models reached 66.51% balanced accuracy when distinguishing between those 6 sites of cancer origin and 90.5% balanced accuracy on a location-specific dataset where cancer types from close locations were grouped. The developed models were further investigated with an explainable artificial intelligence-based approach (XAI) - SHAP. They returned a set of 60 genes with the highest impact on the models’ decision-making process. Conclusions: Our results show that deep-learning methods are a promising opportunity for cancer detection and could support clinicians’ decision-making process in finding the solution for the black-box problem. Clinical and Translational Impact Statement— Utilizing TEPs-based liquid biopsies and deep learning, our study offers a novel approach to early cancer detection, highlighting cancer origin. The integration of Explainable AI reinforces trust in predictive outcomes. Category: Early/Pre-Clinical Research.

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Autorzy (8)

Maksym Albin Jopek
- Uniwersytet Gdański
Krzysztof Pastuszak mgr inż.
Sebastian Cygert dr inż.
- Wydział Elektroniki, Telekomunikacji i Informatyki
- Politechnika Gdańska
Myron G Best dr
- Vrije Universiteit Amsterdam
Thomas Würdinger prof.
- Vrije Universiteit Amsterdam
Jacek Jassem Prof.
- GUMed
Anna Żaczek dr hab.
- GUMed
Anna Supernat dr
- GUMed

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Wersja publikacji: Accepted albo Published Version
DOI:: Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1109/JTEHM.2024.3360865
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Publikacja w czasopiśmie

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artykuły w czasopismach

Opublikowano w:

IEEE Journal of Translational Engineering in Health and Medicine-JTEHM nr 12, strony 306 - 313,
ISSN: 2168-2372

Język:

angielski

Rok wydania:

2024

Opis bibliograficzny:

Jopek M. A., Pastuszak K., Cygert S., Best M. G., Würdinger T., Jassem J., Żaczek A., Supernat A.: Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data// IEEE Journal of Translational Engineering in Health and Medicine-JTEHM -Vol. 12, (2024), s.306-313

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