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Improving platelet‐RNA‐based diagnostics: a comparative analysis of machine learning models for cancer detection and multiclass classification
Abstrakt
Liquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost-effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine-learning techniques are increasingly gaining attention in sample analysis, especially for multidimensional data such as RNA expression profiles. Yet, there is no agreement in the community on which methods are the most effective or how to process the data. To circumvent this, we performed a large-scale study using various machine-learning techniques. First, we took a closer look at existing datasets and filtered out some patients to assert data collection quality. The final data collection included platelet RNA samples acquired from 1397 cancer patients (17 types of cancer) and 354 asymptomatic, presumed healthy, donors. Then, we assessed an array of different machine-learning models and techniques (e.g., feature selection of RNA transcripts) in pan-cancer detection and multiclass classification. Our results show that simple logistic regression performs the best, reaching a 68% cancer detection rate at a 99% specificity level, and multiclass classification accuracy of 79.38% when distinguishing between five cancer types. In summary, by revisiting classical machine-learning models, we have exceeded the previously used method by 5% and 9.65% in cancer detection and multiclass classification, respectively. To ease further research, we open-source our code and data processing pipelines (https://gitlab.com/jopekmaksym/improving-platelet-rna-based-diagnostics), which we hope will serve the community as a strong baseline.
Cytowania
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Autorzy (7)
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Maksym Albin Jopek
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Anna J. Żaczek
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Matthew T. Rondina prof.
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Anna Supernat dr
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Pełna treść
- Wersja publikacji
- Accepted albo Published Version
- DOI:
- Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1002/1878-0261.13689
- Licencja
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otwiera się w nowej karcie
Słowa kluczowe
Informacje szczegółowe
- Kategoria:
- Publikacja w czasopiśmie
- Typ:
- artykuły w czasopismach dostępnych w wersji elektronicznej [także online]
- Opublikowano w:
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Molecular Oncology
ISSN: 1574-7891 - Język:
- angielski
- Rok wydania:
- 2024
- Opis bibliograficzny:
- Jopek M. A., Pastuszak K., Sieczczyński M., Cygert S., Żaczek A. J., Rondina M. T., Supernat A., Improving platelet‐RNA‐based diagnostics: a comparative analysis of machine learning models for cancer detection and multiclass classification, Molecular Oncology, 2024,10.1002/1878-0261.13689
- DOI:
- Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1002/1878-0261.13689
- Źródła finansowania:
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- Spoza PG, koszty OA pokryte przez współautorów
- Weryfikacja:
- Politechnika Gdańska
wyświetlono 45 razy
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